Promoterless cassettes for expression of alphavirus structural proteins

ABSTRACT

The present invention provides an isolated RNA molecule comprising: a) an alphavirus 5′ replication recognition sequence, wherein at least one initiation codon has been removed from the 5′ replication recognition sequence; b) a nucleotide sequence encoding an alphavirus structural protein; and c) an alphavirus 3′ replication recognition sequence, with the proviso that the RNA molecule does not contain a promoter that directs transcription of the nucleotide sequence of (b), and wherein the alphavirus 5′ and 3′ replication recognition sequences of (a) and (c) direct replication of the RNA molecule in the presence of alphavirus nonstructural proteins.

STATEMENT OF PRIORITY

The present invention claims the benefit, under 35 U.S.C. §119(e), ofU.S. Provisional Application No. 60/936,637, filed Jun. 21, 2007, theentire contents of which are incorporated by reference herein.

STATEMENT OF GOVERNMENT SUPPORT

Aspects of this invention were supported by funding under Grant No. 5UO1 A1057286-03 from the National Institutes of Health. The U.S.Government has certain rights in this invention.

FIELD OF THE INVENTION

The present invention relates to improved constructs for and methods ofmaking recombinant alphavirus particles.

BACKGROUND OF THE INVENTION

Alphaviruses are currently being used as vector platforms to developvaccines for infectious diseases and cancer (e.g., see U.S. Pat. Nos.5,792,462; 6,156,558; 5,811,407; 6,531,135; 6,541,010; 6,783,939;6,844,188; 6,982,087; 7,045,335; 5,789,245; 6,015,694; 5,739,026; Pushkoet al., Virology 239(2):389-401 (1997), Frolov et al., J. Virol.71(1):248-258 (1997); Smerdou and Liljestrom, J. Virol. 73(2):1092-1098(1999)). Alphaviruses comprise a genus in the Togaviridae family, andmembers of the genus are found throughout the world, in both vertebrateand invertebrate hosts. Among the most studied alphaviruses for vectorplatforms are Venezuelan Equine Encephalitis (VEE) Virus, Semliki ForestVirus (SFV), and Sindbis Virus (SV), the prototype member of the genus.

One such vector platform is the alphavirus replicon system, described inU.S. Pat. No. 6,190,666 to Garoff et al., U.S. Pat. Nos. 5,792,462 and6,156,558 to Johnston et al., U.S. Pat. Nos. 5,814,482, 5,843,723,5,789,245, 6,015,694, 6,105,686 and 6,376,236 to Dubensky et al; U.S.Published Application No. 2002-0015945 A1 (Polo et al.), U.S. PublishedApplication No. 2001-0016199 (Johnston et al.), Frolov et al. (1996)Proc. Natl. Acad. Sci. USA 93:11371-11377 and Pushko et al. (1997)Virology 239:389-401. An alphavirus replicon vector is engineered tocontain and express one or more nucleic acids of interest, where thenucleic acid of interest can encode, for example, an antigen, acytokine, a ribozyme, or an enzyme. The alphavirus replicon vector canbe derived from any alphavirus, such as Venezuelan Equine Encephalitis(VEE) virus, Sindbis virus, e.g., strain TR339, South African AibovirusNo. 86, and Semliki Forest virus, among others. The vector is thenintroduced into cells in culture that allow replication of alphavirusesand in which the structural proteins of the alphavirus are alsoexpressed, so that the vector is packaged by the alphavirus structuralproteins into alphavirus replicon particles (ARPs). ARPs are thenharvested from the culture and delivered into subjects for a variety oftherapeutic purposes.

Various constructs have been developed to enhance immunogenicity andeffectiveness of the ARP system in vaccine applications. Many of theseconstructs have also been designed to decrease the likelihood offormation of replication-competent alphavirus through recombination ofgenome fragments. Johnston et al. (U.S. Pat. Nos. 5,792,462 and6,156,558) recognized the potential for recombination from a singlehelper system (in which the complete set of structural protein genes ofan alphavirus are on one RNA molecule and the nonstructural proteingenes and heterologous nucleic acid of interest are on a separatereplicon RNA), and thus designed “double-helper” systems that utilizedtwo helper RNAs to encode the structural proteins. Dubensky et al. (U.S.Pat. No. 5,789,245) and Polo et al. (U.S. Pat. No. 6,242,259) describethe use of two DNA alphavirus structural protein expression cassettes,stably transformed into a packaging cell line, to package alphavirusvectors by production of RNAs expressing those structural proteins uponintroduction of a replicating alphavirus vector into cultures of thepackaging cell. Liljestrom and colleagues have presented data confirmingthat a “single helper system” will generate wild-type alphavirusparticles (Berglund, et al. Biotechnology 11(8): 916-920 (1993)). Smithet al have described other novel RNA helpers that direct expression ofthe structural proteins (WO 2004/085660).

By distributing the viral coding sequences among three nucleic acids,two of which comprise the helper system, as described above, thetheoretical frequency of recombination that would create areplication-competent virus (“RCV”) is reduced significantly relative tosingle helper systems. These systems include the use of the alphaviralsubgenomic promoter, often referred to as the 26S promoter or the viraljunction region promoter, to provide a construct which functions as anindependent transcriptional unit and the use of the alphavirus RNApolymerase recognition signals, so that the helper systems can takeadvantage of the presence of the alphavirus replication machinery foramplification and efficient expression of helper functions.

In existing systems, known packaging signals are typically included inreplicon RNAs and excluded from helper constructs. However, helper RNAsare nonetheless packaged or copackaged at a lower frequency (Lu andSilver. J. Virol Methods, 91(1):59-65 (2001)), and helper constructswith terminal recognition signals will be amplified and expressed in thepresence of a replicon, potentially yielding recombination events withother helper molecules or the replicon RNA.

Animal studies with alphavirus replicon particles have employed dosesranging from 10⁵ to 10⁸, with 10⁷, 5×10⁷ and 10⁸ having been effectivelyemployed in non-human primates, which are also the doses being used inhuman clinical trials. In addition, higher doses such as 2×10⁸, 5×10⁸and 10⁹ are also useful in applications for humans. Such dosages requirelarge scale manufacturing procedures, and at such scale, it isstatistically possible that replication-competent alphavirus may begenerated with existing RNA helper systems.

Thus, there remains a need in the art to provide improved systems formanufacturing alphavirus replicon particles to further reduce thepredicted frequency for formation of replication-competent alphavirus,and to optimize manufacturing strategies and costs.

The present invention provides alphavirus RNA helper molecules encodingalphavirus structural proteins that lack a promoter sequence, therebysignificantly decreasing the theoretical number of functionalrecombination events that might occur between the helper molecules andthe replicon vector, resulting in a decrease in the theoreticalprediction for the rate of formation of replication-competent alphavirusduring the production of recombinant alphavirus particles.

SUMMARY OF THE INVENTION

The present invention provides an isolated RNA molecule comprising: a)an alphavirus 5′ replication recognition sequence, wherein an initiationcodon has been removed from the 5′ replication recognition sequence; b)a nucleotide sequence encoding an alphavirus structural protein; and c)an alphavirus 3′ replication recognition sequence, with the proviso thatthe RNA molecule does not contain a promoter that directs transcriptionof the nucleotide sequence of (b), and wherein the alphavirus 5′ and 3′replication recognition sequences direct replication of the entire RNAmolecule in the presence of alphavirus nonstructural proteins.

Additionally provided herein is a method of making an alphavirusreplicon particle, comprising introducing one or more of the RNAmolecules of this invention into a cell, whereby the combination of RNAmolecules encodes all alphavirus structural proteins necessary forproduction of an alphavirus replicon particle, along with an alphavirusreplicon RNA, under conditions whereby alphavirus replicon particles areproduced.

Further provided is a method of making an alphavirus replicon particle,comprising introducing into a cell: a) an alphavirus replicon RNA; b)one or more of the RNA molecules of this invention; and c) one or morepromoter-assisted alphavirus helper constructs, whereby the combinationof RNA molecules of (b) and helper constructs of (c) encodes allalphavirus structural proteins necessary for production of an alphavirusreplicon particle, under conditions whereby an alphavirus repliconparticle is produced.

In additional embodiments, the present invention provides a populationof alphavirus replicon particles, wherein the population contains nodetectable replication-competent virus particles, as determined bypassage on permissive cells in culture.

Also provided herein is a population of alphavirus replicon particles,wherein the population contains no detectable replication-competentvirus particles, as determined by passage on permissive cells inculture, wherein the alphavirus replicon particles comprise one or moreattenuating mutations in either an alphavirus structural protein or analphavirus nonstructural protein or both an alphavirus structuralprotein and an alphavirus nonstructural protein.

Furthermore, the present invention provides a method of inducing animmune response in a subject, comprising administering an effectiveamount of the population of alphavirus replicon particles of thisinvention to the subject.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the structure of the 5′ replication recognition sequence(RRS) of a full length (FL) promoterless helper molecule. The locationof start codons upstream of the capsid or glycoprotein (GP) initiationcodons within the 5′ replication recognition sequence are indicated withoutlined lines and black lines. Outlined lines indicate start codonsthat are in-frame with the coding sequence for capsid or GP. Black linesindicate start codons that are out-of-reading frame with the codingsequence for capsid or GP. Numbers under the vertical lines indicate thefirst nucleotide positions for the putative start codons in the 5′replication recognition sequence, numbered from the 5′ terminus of themolecule.

FIG. 2 shows the structure of 5′ replication recognition sequencedeletions in a promoterless helper molecule. The outlined boxes indicatethe 5′ replication recognition sequence remaining in each construct andthe number inside the box is the nucleotide length of the sequence. Thinblack lines indicate the 5′ replication recognition sequence that hasbeen deleted from each construct. Boxes with diagonal stripes representthe location of the coding sequence for either capsid or GP.

FIG. 3 is a Northern blot analysis. Total cellular RNA was extractedfrom Vero cells electroporated with 30 μg of pERK/342/MS/BoNT A repliconmRNA and either 30 μg of dHE1-6M1 (a promoterless E1 helper) or 30 μg ofa GP helper RNA containing a 26S promoter (13.4.6). RNA for each sample(5 μg) was run on a 1% glyoxal gel and transferred to a BrightStar®membrane (Ambion; Austin, Tex.). A probe specific for the genomic sensealphavirus RNA 3′ end was used to detect replication of the helpers.Lane 1: RNA molecular weight marker, lane 2: dHE1-6M1 helper+BoNT Areplicon, lane 3: promoter-assisted GP helper+BoNT A replicon.

FIG. 4 is a diagram showing the C-terminal amino acid and nucleotidesequence of the ubiquitin monomer and N-terminal residues of alphaviruscapsid and glycoprotein coding sequences for ubiquitinated (dHcapU, SEQID NO:99, and dHgpU, SEQ ID NO:100) or standard (dHcap, SEQ ID NOs:101and 102, and dHgp, SEQ ID NOs:103 and 104) constructs. The “Met Phe,”“Pro Met Phe,” “Pro Thr Met Ser (SEQ ID NO:105),” and “Thr Met Ser” atthe right end of these sequences represent amino acids found at theN-terminus of the capsid and GP proteins. The ubiquitinated constructshave additional N-terminal residues not found in the 13.2.2 and 13.4.6helpers. The right-most box indicates the 3′ RsrII restriction site andamino acids coded as a result of the primary nucleotide sequence. Theleft-most box represents critical residues for cleavage of ubiquitinfrom VEE structural proteins and indicates the portion of the nucleotidesequence (SEQ ID NO:106) encoding these residues.

FIG. 5 shows Western blot analyses (one using capsid-specific antibodyand the other using glycoprotein (GP)-specific antibody) of cell lysatesgenerated from cells electroporated to produce VRP in a packaging study(Table 10). Two RNA helpers, in addition to a replicon, wereelectroporated into the cells as follows: Lane 1, dHcap6-mut1 and 13.4.6(GP); Lane 2, Hcap4 and dHgp6-mut1; Lane 3, dHcapU and dHgpU; Lane 4,dHcap(FL) and dHgp(FL); Lane 5, Hcap4 and dHgpU; Lane 6, Hcap4 anddHgp(FL); Lane 7, dHcapU and 13.4.6; Lane 8, dHcap(FL) and 13.4.6; Lane9, Hcap4 and 13.4.6; Lane 10, molecular weight markers.

FIG. 6 shows a Northern blot analysis of capsid helper RNAs produced inVero cells into which two RNA helpers, in addition to a replicon, wereelectroporated into the cells as follows: Lane 1, dHcap6-mut1 and 13.4.6(GP); Lane 2, Hcap4 and dHgp6-mut1; Lane 3, dHcapU and dHgpU; Lane 4,dHcap(FL) and dHgp(FL); Lane 5, Hcap4 and dHgpU; Lane 6, Hcap4 anddHgp(FL); Lane 7, dHcapU and 13.4.6; Lane 8, dHcap(FL) and 13.4.6. Thetranslatable capsid RNA molecule in each lane is marked with anasterisk.

FIG. 7 shows a Northern blot analysis of glycoprotein (GP) helper RNAsproduced in Vero cells into which two RNA helpers, in addition to areplicon, were electroporated into the cells as follows: Lane 1,dHcap6-mut1 and 13.4.6 (GP); Lane 2, Hcap4 and dHgp6-mut1; Lane 3,dHcapU and dHgpU; Lane 4, dHcap(FL) and dHgp(FL); Lane 5, Hcap4 anddHgpU; Lane 6, Hcap4 and dHgp(FL); Lane 7, dHcapU and 13.4.6; Lane 8,dHcap(FL) and 13.4.6. The translatable glycoprotein RNA molecule in eachlane is marked with an asterisk.

DETAILED DESCRIPTION OF THE INVENTION

As used herein, “a,” “an” and “the” can mean one or more than one,depending on the context in which it is used. For example, “a” cell canmean one cell or multiple cells.

Also as used herein, “and/or” refers to and encompasses any and allpossible combinations of one or more of the associated listed items, aswell as the lack of combinations when interpreted in the alternative(“or”).

Furthermore, the term “about,” as used herein when referring to ameasurable value such as an amount of a compound or agent of thisinvention, dose, time, temperature, and the like, is meant to encompassvariations of ±20%, ±10%, ±5%, ±1%, ±0.5%, or even ±0.1% of thespecified amount.

The terms “5′ alphavirus replication recognition sequence,” “3′alphavirus replication recognition sequence,” “5′ replicationrecognition sequence,” and “3′ replication recognition sequence refer tothe RNA sequences found in alphaviruses, sequences derived therefrom, orsynthetic sequences based on conserved sequences among variousalphaviruses, that are recognized by the nonstructural alphavirusreplicase proteins and lead to replication of viral RNA. In someembodiments, these sequences can be in the form of DNA to facilitate thepreparation, mutation and/or manipulation of the constructs, plasmidsand nucleic acids of this invention to produce VRPs. These sequences arealso referred to as the “5′ and 3′ ends,” 5′ and 3′ viral sequencesrequired for nonstructural protein-mediated amplification, 5′ and 3′sequences required for nonstructural protein-mediated amplification, 5′or 3′ conserved sequence element (CSE), 5′ or 3′ non-coding regions, 5′or 3′ noncoding region sequences, 5′ or 3′ viral sequences required incis for replication, 5′ or 3′ sequence that initiates transcription ofan alphavirus, and/or alphavirus 5′ and 3′ sequences, with the 5′ and 3′designations referring to their location in the alphavirus genome. Inthe nucleic acid molecules of this invention, the use of these 5′ and 3′ends will result in replication and/or transcription of the RNA sequenceencoded between the two ends. These sequences can be modified bystandard molecular biological techniques (e.g., truncated at either endand/or modified to remove initiation (i.e., start) codons or to enhancetranslatability) to further minimize the potential for recombinationand/or to introduce cloning sites, etc., with the proviso that they muststill be recognized by the alphavirus replication machinery.

As used herein, the terms “initiation codon” or “start codon” refer to acodon that is AUG in RNA and ATG in DNA that may or may not be used inthe translation of a functional protein.

The term “alphavirus structural protein/protein(s)” refers to one or acombination of the structural proteins encoded by alphaviruses. Theseare produced by the wild type virus as a polyprotein and are describedgenerally in the literature as C-E3-E2-6k-E1. E3 and 6k serve asmembrane translocation/transport signals for the two glycoproteins, E2and E1. Thus, use of the term E1 herein can refer to E1, E3-E1, 6k-E1,or E3-6k-E1, and use of the term E2 herein can refer to E2, E3-E2,6k-E2, PE2, p62 or E3-6k-E2. The term “glycoprotein helper” or “GPhelper” typically refers herein to a helper molecule that encodes bothE2 and E1 glycoproteins; in certain embodiments of this invention, E1and E2 are encoded on separate helper molecules.

The terms “helper(s)” and “helper molecules” are used interchangeablyand refer to a nucleic acid molecule that expresses nucleic acidencoding one or more alphavirus structural proteins.

The terms “helper cell” and “packaging cell” are used interchangeablyherein and refer to a cell in which alphavirus replicon particles areproduced. The helper cell comprises a set of helper molecules and/orhelper constructs as described herein that encode one or more alphavirusstructural proteins. The helpers can be RNA or DNA or both. The helpercell or packaging cell can be any cell that is alphavirus-permissive,i.e., that can produce alphavirus particles upon introduction of areplicon RNA. Alphavirus-permissive cells include, but are not limitedto, Vero, baby hamster kidney (BHK), 293, 293T/17 (ATCC accession numberCRL-11268), chicken embryo fibroblast (CEF), UMNSAH/DF-1 (ATCC accessionnumber CRL-12203) and Chinese hamster ovary (CHO) cells.

A “promoter” as used herein is a nucleic acid sequence that directstranscription of an RNA molecule.

An “isolated cell” as used herein is a cell or population of cells thathave been removed from the environment in which the cell occursnaturally and/or altered or modified from the state in which the celloccurs in its natural environment. An isolated cell of this inventioncan be a cell, for example, in a cell culture. An isolated cell of thisinvention can also be a cell that can be in an animal and/or introducedinto an animal and wherein the cell has been altered or modified, e.g.,by the introduction into the cell of an alphavirus particle of thisinvention.

As used herein, an “alphavirus subgenomic promoter” or “26S promoter” isa promoter as originally defined in a wild type alphavirus genome thatdirects transcription of a subgenomic messenger RNA as part of thealphavirus replication process.

The heterologous nucleic acid (e.g., a gene of interest or “GOI” ornucleic acid of interest or “NOI”) used in some embodiments of thisinvention is a nucleic acid that is not present in the genome of a wildtype alphavirus and/or is not present in the genome of a wild typealphavirus in the same order as it exists in a recombinant nucleic acidof this invention. For example, in certain embodiments, the NOT canencode one or more alphavirus structural proteins (e.g., C, PE2/E2, E1,E3, 6K) when they are used as helper nucleic acids in the assembly ofinfectious, defective alphavirus particles (e.g., alphavirus repliconparticles) or as immunogens for vaccines against diseases caused bycertain alphaviruses.

The present invention is based on the surprising and unexpecteddiscovery that RNA molecules comprising a nucleotide sequence encodingalphavirus structural protein(s) and alphavirus 5′ and 3′ sequences,wherein an initiation codon has been removed from the 5′ replicationrecognition sequence, but lacking a promoter sequence (e.g., asubgenomic alphavirus promoter sequence, sometimes referred to as a 26S,or viral junction region, promoter) can be replicated such that thefull-length positive strand RNA can be translated efficiently andproduce sufficient amounts of alphavirus structural proteins in transfor the production of alphavirus replicon particles in cultured celllines. These “promoterless” RNA molecules, sometimes referred to hereinas “Δ26S helpers,” increase the theoretical safety margin in apopulation of alphavirus replicon particles (e.g., produced for use as avaccine or adjuvant) by decreasing the predicted theoretical frequencyof generation of functional recombination events that occur between thehelper molecules and the replicon vector.

Any split helper system requires a minimum of two independentrecombination events to generate replication-competent alphavirus (RCV).For alphaviruses, recombination is thought to be predominantly theresult of random strand switching by the RNA replication complex (Weisset al 1991), although homologous recombination has also been reported.For the first recombination event, the replication complex could, forexample, begin at the 3′ end of an RNA helper molecule in the splithelper/replicon packaging systems disclosed in the literature (e.g.,Johnston et al. U.S. Pat. No. 5,792,462). If the complex continuedreplication of this helper RNA through the 26S or viral junction regionand then switched to the foreign nucleotide sequence in the replicon RNAas a template and completed replication through the replicon 5′ end, theresulting “recombinant replicon intermediate” would contain sequenceencoding all the non-structural proteins, some or all of thetranscriptional unit containing the foreign nucleic acid of interest(NOI) coding region, and the new inserted transcriptional unitexpressing one of the alphaviral structural proteins. In order for anRCV to be created, a subsequent, second recombination event must occurby a strand-switching event into the 3′ replication recognition sequenceof the recombinant replicon intermediate (described above), since thisis the only location that would result in retention of functionaltranscriptional units for all of the nonstructural and structuralprotein coding sequences without insertional mutagenesis. Because thehelper RNA molecules contain 26S promoters, two such recombinationevents could create, theoretically, an RCV. The precise recombinationpoints would not be critical because each of the recombination insertswould be an independent transcriptional unit.

Generation of RCV using promoterless helper molecules of this inventionwould also require a minimum of two independent recombination events,but the constraints for obtaining a functional recombinant are muchhigher than for the RNA helper molecules known in the literature andthus the theoretical frequency for generating RCV is much lower. This isbecause, in the absence of the 26S promoter, most recombination eventswould not result in the generation of a functional transcriptional unitthat could express an alphavirus structural protein. Thus, thegeneration of RCV using promoterless helper molecules will require theregeneration of a structural polyprotein open reading frame (i.e.,substantively similar to the structure found in the wild-type virus fromwhich these helpers are derived), and this in turn requires that the tworequired recombination events occur in a specific order and in veryspecific nucleotide locations. The initial recombination event mustinvolve the capsid helper coding sequence, since it must be located in aproper (i.e., 5′) position relative to the glycoproteins in order tocleave itself and generate a functional capsid protein. The capsidhelper must be recombined with the replicon vector via a nucleotide- ornear-nucleotide-perfect recombination event to achieve a recombinant inwhich there would be expression of the capsid protein from the replicon26S promoter. That is, only recombinations that 1) are directlydownstream of the replicon 26S promoter, 2) are in frame with anyremnants of the heterologous GOI, and 3) do not result in the generationof a GOI/alphavirus capsid fusion protein (thereby generating aninactive alphavirus capsid), would be functional. The secondrecombination event, involving the alphavirus glycoprotein helper, isunder the same constraints as the first, in addition to being limited tooccurring in the 3′ replication recognition sequence. Thus, methods ofthis invention for producing the particles using the promoterless helpermolecules will theoretically generate RCV at a much lower frequency thanthe helper molecules known in the literature, a frequency so low that nosuch RCV have been detected with the methods of this invention.

The surprising nature of this invention lies in the fact that previousefforts to produce helper/replicon systems for assembling alphavirusparticles have relied on the use of a strong promoter, most often thealphavirus 26S subgenomic promoter, to provide sufficient RNA moleculesfrom which to translate structural proteins for assembly. In starkcontrast to the existing literature, the inventors discovered that theycan utilize novel RNA helper molecules that can be translated directlyas full length molecules without transcription of smaller messenger RNAsfrom the 26S promoter and the messenger amplification that normallyaccompanies this process in wild-type alphavirus propagation and helperRNA systems known in the literature. Direct translation of the helperRNAs of this invention is then accomplished through the recognition ofthe cap at the 5′ end of the full-length RNA by cellular ribosomalmachinery. Within a eukaryotic cell, the initiation of translation froman mRNA involves a series of tightly regulated events that allow therecruitment of ribosomal subunits to the mRNA. In the case ofcap-dependent translation, the methyl-7-G(5′)pppN structure present atthe 5′ end of the mRNA, known as “cap,” is recognized by the cellularinitiation factor eIF4F, which is composed of eIF4E, eIF4G and eIF4A.(reviewed in Hershey & Merrick. Translational Control of GeneExpression, pp. 33-88. Cold Spring Harbor, N.Y.: Cold Spring HarborLaboratory Press. 2000.)

Alphaviruses are positive strand RNA viruses; when the viral RNA entersthe cell, translation of the nonstructural alphavirus proteins (nsP1,nsP2, nsP3 and nsP4) occurs from this RNA, and these proteins generate afull-length negative strand RNA template, respectively. The negativestrand RNA is then replicated to produce a full-length (“genomic”)positive strand RNA and a smaller (“subgenomic”) positive strand that isinitiated at the 26S promoter. When the positive strands are produced,the nonstructural proteins of the alphavirus also cap the RNA, making itavailable in the cytoplasm for translation by ribosomes. The “cap”refers to a methylated residue added to the 5′ end of the RNA. Inspecific embodiments of this invention, the helper RNA molecules thatare produced in vitro (which are positive strand RNAs) are not capped.When the positive strand helper RNAs are introduced into a eukaryoticcell also containing a replicon RNA, largely negative strand synthesisoccurs initially. In the presence of the alphavirus replicon RNA, fromwhich the non-structural proteins are synthesized, the negative strandtemplates (both helper and replicon) will be replicated into positivestrand RNAs that are then capped. In other embodiments of thisinvention, the helper RNAs can be capped in vitro, using reagents wellknown to the art and commercially available, for example, from Promega(Madison, Wis.) and Ambion (Austin, Tex.). Caps can include G cap, Ccap, A cap, methylated G (m⁷G(5′ppp(5′)pppG(5)A); unmethylatedG(G(5′ppp(5′)A); ARCA (anti-reverse cap analog, 3-O-Me-m⁷G(5′)pppG(5));trimethylated (m²,^(2,7)G(5′ppp(5′)pppG), 2-way cap (m⁷G(5′ppp(5′)m⁷G),for example. In some embodiments, for maximal yield of ARP, all helpersof this invention used to produce ARP are either capped or uncapped.Highest yields have been recorded with capped helper RNAs, but, incertain embodiments, uncapped helper RNAs can generate sufficiently highyields such that the added cost of capping may be avoided. It is alsopossible to cap only one of the helper RNAs, although this also maysometimes limit ARP yields. In general, the inventors have shown thatARP yield can be optimized by routine experimentation looking at severalvariables, such as varying the use of capping, the ratio of cap analogto NTPs in the transcription mixture, and the ratio of RNAs used togenerate the ARPs.

Thus, in particular embodiments, the present invention provides anisolated RNA molecule comprising, consisting essentially of and/orconsisting of: a) an alphavirus 5′ replication recognition sequencewherein at least one initiation codon has been removed; b) a nucleotidesequence encoding an alphavirus structural protein; and c) an alphavirus3′ replication recognition sequence, with the proviso that the RNAmolecule does not contain a promoter that directs transcription of thenucleotide sequence of (b), and wherein the alphavirus 5′ and 3′replication recognition sequences direct replication of the entire RNAmolecule in the presence of alphavirus nonstructural proteins.

A wide variety of nucleic acid sequences can satisfy the function of the5′ and 3′ ends in the nucleic acid constructs of this invention. Forexample, the sequence can include the alphavirus 5′ replicationrecognition sequence and other adjacent sequences, as exemplified above,for the VEE alphavirus. Additionally, deletions can be made in thenative 5′ alphavirus end to remove certain secondary structuralelements, for example stem-loop structures. In certain embodiments, oneor more of these stem-loop structures may be removed from the helperconstructs of this invention. Alternatively, non-alphavirus or othersequences can be employed as this element, while maintaining similarfunctional capacity, for example, in the case of Sindbis virus,nucleotides 10-75 for tRNA asparagine (Schlesinger et al. U.S. Pat. No.5,091,309).

In some embodiments, the 3′ alphavirus replication recognition sequencecan be approximately 300 nucleotides in length, which containsessentially the native alphavirus 3′ replication recognition sequence.The minimal 3′ replication recognition sequence, conserved amongalphaviruses, is a 19 nucleotide sequence (Hill et al., Journal ofVirology, 2693-2704 (1997)). In addition, for Sindbis virus, it has beenshown that the poly(A) tail immediately following the 3′ replicationrecognition sequence must be at least 11-12 residues in length and thatthe 3′ 13 nt of the 3′ replication recognition sequence are critical forefficient minus strand RNA synthesis (Hardy and Rice, Journal ofVirology, 79:4630-4639 (2005)). Therefore, sequence for the 3′ end caninclude a complete alphavirus 3′ replication recognition sequence, or atruncated region of the 3′ replication recognition sequence, which stillmaintains function as a recognition sequence, or a 3′ end that isbetween 25 and 325 nucleotides in length and contains a poly(A) runimmediately following the 3′ replication recognition sequence with aminimum length of 11-12 nt. Other examples of sequences that can be usedin this context include, but are not limited to, non-alphavirus or othersequences that maintain a similar functional capacity to permitinitiation of negative strand RNA synthesis (e.g., sequences describedin George et al. J. Virol. 74: 9776-9785 (2000)).

The 5′ and 3′ replication recognition sequences used in the RNAmolecules of this invention can be derived from the same or differentalphaviruses in any combination, and they can be used in any combinationwith replicon vectors which are derived from the same or differentalphaviruses.

In certain embodiments of this invention, the 5′ and 3′ sequences of thehelper RNA molecules are chosen to both maximize the performance of thehelpers in generating VRPs and minimize the theoretical potential forgenerating RCV. Specific embodiments may include modifications of the 5′and 3′ sequences as well as deletions of parts of the original 5′ and 3′sequences from the alphavirus, examples of which are described herein.There are numerous combinations of 5′ and 3′ sequences described in thisinvention, and different combinations can be used for each helpermolecule. It is within one of skill in the art to test variouscombinations of the modifications and deletions taught herein todetermine their performance in the generation of VRPs.

The RNA helper molecules of this invention rely on ribosomes scanningfrom the 5′ cap structure through the 5′ replication recognitionsequence to initiate translation of the alphavirus structural proteinsat their native methionine start codon. The presence of additionalinitiation codons in these regions reduces the effectiveness of thesehelpers by allowing translation to initiate at a site other than thenative start codon for the structural proteins, thereby generatingeither fusion proteins as the ribosomes move along the mRNA into thealphavirus structural protein coding region or short non-functionalpeptides when the ribosomes subsequently reach a stop codon in the 5′replication recognition sequence. Therefore, the use of the intact 5′alphavirus non-coding region in these helpers (i.e., the entire sequencefrom the 5′ terminus of the wild-type alphavirus up to the first codonof the 26S subgenomic promoter) is not optimal, due to the presence ofnumerous start and stop codons in this region. Thus, in particularembodiments, the RNA molecules of this invention can have one or moreinitiation codons removed from the 5′ replication recognition sequence.By one or more is meant that two, three, four, five, six, seven, eight,nine, ten, 11, 12 or more initiation codons (i.e., start codons) havebeen removed or inactivated according to methods standard in the art.

Thus, the present invention provides an RNA molecule of this inventionwherein one or more initiation codons have been removed, e.g., bymutation from AUG to GUG, from the 5′ replication recognition sequence.In a specific embodiment, an RNA molecule is provided wherein allinitiation codons have been removed, e.g., by mutation from AUG to GUG,from the 5′ replication recognition sequence. For example, one or moreinitiation codons in any combination at the following positions as shownin FIG. 1 can be removed, e.g., mutated: 12, 45, 148, 154, 160, 258,294, 299, 331, 390, 411, 441 and 499.

By removal of an initiation codon it is meant that the nucleotidesequence is modified (e.g., according to methods described herein and asknown in the art) to delete or change the initiation codon, therebyremoving or altering initiation or activity (e.g., translation activity)at that site. In some embodiments, a majority of the initiation codonscan be removed, but it is possible that only a few of such codons in the5′ region of a particular helper construct are in a context that istypically recognized by a ribosome. Thus, for specific 5′ sequences,removal of 2-3 such codons, out of a possible 10-12 codons, may resultin expression levels that are not significantly different than aconstruct in which all 10-12 codons have been removed. It is within thescope of this invention that there are a numerous specific 5′ sequences,derived from the wild-type alphavirus sequences, that when used in thehelper molecules of this invention, will result in sufficient expressionwithin the packaging or helper cell to provide acceptable yields ofalphavirus replicon particles.

The RNA molecule of this invention can comprise a nucleotide sequenceencoding 1) an alphavirus capsid protein, 2) alphavirus E1 and E2proteins in any order, 3) alphavirus capsid protein and alphavirus E1protein in any order, 4) alphavirus capsid protein and alphavirus E2protein in any order, 5) alphavirus E2 protein, and/or 6) alphavirus E1protein. In other embodiments, a single RNA molecule of this inventioncan encode the three alphavirus structural proteins, i.e., capsidprotein, alphavirus E1 protein and alphavirus E2 protein, in any order.In some embodiments, the RNA molecule of this invention can specificallyexclude a nucleotide sequence encoding an alphavirus structural protein(e.g., the molecule can specifically exclude a nucleotide sequenceencoding capsid, alphavirus E1 protein, alphavirus E2 protein or anycombination of capsid, E1 protein and E2 protein).

In various embodiments of this invention, the RNA molecule can comprisesequence from the 5′ end of Venezuelan equine encephalitis (VEE) virus,which includes a 5′ replication recognition sequence. As described byPushko et al. (1997), the 5′ replication recognition sequence of VEEpromoter-assisted helpers typically consists of 575 nucleotides (nt) ofVEE sequence. The first 519 are contiguous and represent the 44 ntuntranslated region (UTR) and the first 475 nt of nsP1 (44+475=519). Theremaining 56 nt encode the last 21 nt of the nsP4 gene (including theTAA stop codon), 7 nt of the minimal 26S promoter (whose sequencepartially overlaps the nsP4 gene) and a 28 nt leader sequence upstreamof the VEE structural protein gene initiation codon (21+7+28=56).

Thus, the complete 5′ replication recognition sequence for thepromoter-assisted helpers described by Pushko et al. (1997) consist of575 nt of VEE sequence. The promoterless helpers of this inventionencode all or a portion of the first 514 nucleotides (nt) found in thepromoter-assisted helpers described above. In addition to the 514 ntdescribed above, sequence encoding an RsrII restriction enzyme site (7nt) is also present just upstream of the structural protein codingsequence start site (ATG in DNA; AUG in RNA). Inclusion of these ntincreases the 5′ replication recognition sequence for the full lengthcapsid helper (dHcap(FL) to 521 nt (not including the A residue of theinitiation codon).

In some examples of the promoterless capsid helpers and all exampleswith promoterless glycoprotein helpers, an additional modification toinclude a near-consensus Kozak sequence (3 nt (ACC)) just upstream ofthe structural protein coding sequence initiation codon but downstreamof the RsrII sequence have been added. Because of the Kozak modificationthe full length glycoprotein helper (dHgp(FL) has a 5′ replicationrecognition sequence of 524 nt. With these nucleotide sequences definedfor the promoterless capsid and glycoprotein helpers as the “fulllength” (“FL”) 5′ VEE sequence for the purposes of the followingdescription, deletions in this sequence result in other embodiments thatencompass the 5′ replication recognition sequence. These embodimentsinclude nucleotides 1 through 141 (not including the A residue of theinitiation codon) of the VEE nucleotide sequence, at a minimum. Withinthe first 200 nucleotides of the 5′ sequence, four stem-loop (SL)structures in the RNA are predicted.

Embodiments of the 5′ sequence useful in the helper constructs of thisinvention may include 1, 2, 3 or all of the SL structures in thisregion. Embodiments that remove the SL2 region, and retain the SL1, SL3and SL4 structures, are useful in the helper constructs of thisinvention. SL structures 1 and 2 are contained in the first 145nucleotides; SL 3 and 4 are present between nucleotides 145 and 200.Thus, in some embodiments, the 5′ replication recognition sequence isincluded in a 5′ non-coding region of the construct which is 524nucleotides in length (e.g., dHgp(FL) in FIG. 2) and in otherembodiments, the 5′ replication recognition sequence can be included ina 5′ non-coding region that is anywhere from 70 (e.g., containing SL1,SL3 and SL4) to 524 nucleotides in length. For example, the 5′replication recognition sequence can be 141, 144 (dH #8) 200, 203 (dH#7), 248, 249 (dH #6), 309, 312 (dH #5), 351, 354 (dH #4), 412, 415 (dH#3) 450, 452 (dH #2), 499 or 502 (dH #1) nucleotides in length,including any number between 70 and 524 not specifically recited herein(e.g., 237, 379, 444, etc.). It should be noted that the exactnucleotide number and length varies somewhat between differentalphaviruses and between different strains of a given alphavirus. It iswell within the ability of one skilled in the art to identify thecorresponding locations of the nucleotides described herein based oncorresponding structure and/or function and/or of the secondarystructures described herein in any alphavirus and create the RNA helpermolecules of this invention as well as the above-described modificationsfrom the primary nucleotide sequence of any alphavirus.

The RNA helper molecules of this invention also comprise sequence fromthe 3′ end of an alphavirus, which in particular embodiments, can be,but is not limited to the Venezuelan equine encephalitis virus, whichincludes the alphavirus 3′ replication recognition sequence. The 3′terminal 19 nucleotides of all alphaviruses are highly conserved, whilethe 3′ sequence between the last codon of the E1 glycoprotein and thehighly conserved 19 nucleotides is less conserved, both in terms oflength and sequence among alphaviruses. The length of the 3′ non-codingregion (including the conserved 19 nucleotides, herein SEQ ID NO:52) canrange from 25 to 325 nucleotides. In specific embodiments of thisinvention, the 3′ sequence is between 73 to 117 nucleotides of the VEE3′ end. In particular embodiments, alphavirus 3′ replication recognitionsequence of this invention can comprise, consist essentially of and/orconsist of the nucleotide sequence of SEQ ID NO:55 (for dHcap(FL)through dHcap7; dHcap(FL)mm through dHcap7 mm, dHcap(FL)mut1 throughdHcap7-mut1), SEQ ID NO:56 (for Hgp(FL) through dHgp7, dHgp(FL)mmthrough dHgp7-mm, dHgp(FL)mut1 through dHgp7-mut1), SEQ ID NO:57 (fordHcap6mut1(w/stop), SEQ ID NO:58 (for dHcap7mut1(w/stop)+19 nt anddHgp7mut1−S+19 nt), and SEQ ID NO:59 (dHcap6mut1(W-stop).

In particular embodiments, the alphavirus 5′ replication recognitionsequence of this invention can comprise, consist essentially of and/orconsist of the nucleotide sequence of SEQ ID NO:1 (dHcap(FL)), SEQ IDNO:2 (dHcap1), SEQ ID NO:3 (dHcap2), SEQ ID NO:4 (dHcap3), SEQ ID NO:5(dHcap4), SEQ ID NO:6 (dHcap5), SEQ ID NO:7 (dHcap6), SEQ ID NO:8(dHcap7), SEQ ID NO:9 (dHcap8), SEQ ID NO:10 (dHgp(FL), SEQ ID NO:11(dHgp1), SEQ ID NO:12 (dHgp2), SEQ ID NO:13 (dHgp3), SEQ ID NO:14(dHgp4), SEQ ID NO:15 (dHgp5), SEQ ID NO:16 (dHgp6), SEQ ID NO:17(dHgp7), SEQ ID NO:18 (dHgp8), SEQ ID NO:19 (dHcap(FL)-mm), SEQ ID NO:20(dHcap1-mm), SEQ ID NO:21 (dHcap2-mm), SEQ ID NO:22 (dHcap3-mm), SEQ IDNO:23 (dHcap4-mm), SEQ ID NO:24 (dHcap5-mm), SEQ ID NO:25 (dHcap6-mm),SEQ ID NO:26 (dHcap7-mm), SEQ ID NO:27 (dHgp(FL)-mm), SEQ ID NO:28(dHgp1-mm), SEQ ID NO:29 (dHgp2-mm), SEQ ID NO:30 (dHgp3-mm), SEQ IDNO:31 (dHgp4-mm), SEQ ID NO:32 (dHgp5-mm), SEQ ID NO:33 (dHgp6-mm), SEQID NO:34 (dHgp7-mm), SEQ ID NO:35 (dHcap(FL)mut1), SEQ ID NO:36 (dHcap1mut1), SEQ ID NO:37 (dHcap2 mut1), SEQ ID NO:38 (dHcap3 mut1), SEQ IDNO:39 (dHcap4 mut1), SEQ ID NO:40 (dHcap5 mut1), SEQ ID NO:41 (dHcap6mut1), SEQ ID NO:42 (dHcap7 mut1), SEQ ID NO:43 (dHgp(FL)mut1), SEQ IDNO:44 (dHgp1 mut1), SEQ ID NO:45 (dHgp2 mut1), SEQ ID NO:46 (dHgp3mut1), SEQ ID NO:47 (dHgp4 mut1), SEQ ID NO:48 (dHgp5 mut1), SEQ IDNO:49 (dHgp6 mut1), SEQ ID NO:50 (dHgp7 mut1), SEQ ID NO:51(dHcap6-mut1-dSL2), SEQ ID NO:52 (dHgp6-mut1-dSL2(-S)); SEQ ID NO:53(dHcapU); and SEQ ID NO:54 (dHgpU). The specific helper for which these5′ sequence examples have been synthesized is given in parentheses. Thesequences can vary slightly in length due to the use of additionalnucleotides to provide a near-optimal Kozak consensus sequence toenhance translation of the structural protein coding sequence in some ofthe helper constructs. (The ATG (AUG in RNA) of the coding region forthe structural protein coding sequence is not included in these 5′sequences). RNA molecules of this invention comprising the nucleotidesequences identified above can be employed in the methods of thisinvention for production of alphavirus replicon particles in anycombination, in any order and/or in any multiplicity.

The present invention additionally provides a vector and/or a nucleicacid construct comprising the RNA molecule of this invention. Furtherprovided is a cell comprising one or more RNA molecules of thisinvention and one or more alphavirus replicon vectors. By one or more ismeant one, two, three, four, five, six, seven, etc. A cell of thisinvention is any cell in which nucleic acid constructs encodingalphavirus proteins can be expressed. Examples of cells of thisinvention include, but are not limited to, Vero, baby hamster kidney(BHK), 293, 293T/17 (ATCC accession number CRL-11268), chicken embryofibroblast (CEF), UMNSAH/DF-1 (ATCC accession number CRL-12203), PERC.6and Chinese hamster ovary (CHO) cells.

Further provided herein is a method of making an alphavirus repliconparticle, comprising introducing one or more of the RNA molecules ofthis invention into a cell, whereby the combination of RNA moleculesencodes all alphavirus structural proteins necessary for production ofan alphavirus replicon particle, along with an alphavirus replicon RNA,under conditions whereby alphavirus replicon particles are produced. Insome embodiments of this invention, the alphavirus particle mimics thestructural make-up of the native alphavirus, in which the replicon RNAis coated with the capsid protein and then enveloped with cell membranecontaining the alphavirus glycoproteins. In such embodiments, thealphavirus structural proteins are all from the same alphavirus. Inalternative embodiments, the alphavirus proteins can be from differentalphaviruses, provided that these different proteins “recognize” eachother during particle assembly or that they are modified (as describedin the literature) so that they will be able to recognize each other.

In some embodiments of the methods of this invention, two RNA moleculesof this invention are introduced into a cell of this invention, whereinthe two RNA molecules encode different alphavirus structural proteins ina combination whereby all the necessary structural proteins are producedin the packaging cell to produce alphavirus replicon particles. Thus,the present invention provides a method wherein two RNA molecules areintroduced into the cell and wherein a first RNA molecule of the two RNAmolecules encodes one or more alphavirus structural proteins but not allof the structural proteins and a second RNA molecule of the two RNAmolecules encodes one or more alphavirus structural proteins that arenot encoded by the first RNA molecule.

Also provided is a method wherein three RNA molecules of this inventionare introduced into a cell, wherein the three RNA molecules each encodea different alphavirus structural protein, in a combination whereby allof the necessary structural proteins are produced in the cell to producealphavirus replicon particles. Thus, a method is provided, wherein threeof the RNA molecules of this invention are introduced into the cell,wherein a first RNA molecule of the three RNA molecules encodes one ormore alphavirus structural proteins but not all of the structuralproteins and a second RNA molecule of the three RNA molecules encodesone or more alphavirus structural proteins that are different from thealphavirus structural proteins encoded by the first RNA molecule and athird RNA molecule of the three RNA molecules encodes one or morealphavirus structural proteins that are different from the alphavirusstructural proteins encoded by the first RNA molecule and the second RNAmolecule. For example, in one embodiment, the first RNA molecule canencode alphavirus capsid protein, the second RNA molecule can encodealphavirus glycoprotein E1 and the third RNA molecule can encodealphavirus glycoprotein E2.

In some embodiments, one or more, but not all, of the alphavirusstructural proteins can be encoded by the replicon RNA that is packagedby the alphavirus structural proteins. For example, a recombinant RNAused in the methods of making alphavirus replicon particles claimedherein can comprise, as a nucleic acid of interest and/or in addition toa nucleic acid of interest, a nucleic acid sequence encoding onealphavirus structural protein or more than one alphavirus structuralprotein. Thus, in a specific embodiment, a replicon RNA encodes analphavirus structural protein or more than one alphavirus structuralprotein. This replicon RNA can be introduced into a population of cellstogether with one or more RNA helper molecules of this invention, suchthat the replicon RNA and the RNA helper molecules(s) produce all of thealphavirus structural proteins, and the replicon RNA is packaged intoparticles in said cells.

In further embodiments, a method is provided for making an alphavirusreplicon particle, comprising introducing into a cell: a) an alphavirusreplicon RNA; b) one or more RNA molecules of this invention; and c) oneor more promoter-assisted alphavirus helper constructs, whereby thecombination of RNA molecules of (b) and helper constructs of (c) encodesall alphavirus structural proteins necessary for production of analphavirus replicon particle, under conditions whereby an alphavirusreplicon particle is produced.

Thus, in additional embodiments of this invention, “promoter-assistedhelper constructs,” i.e., recombinant DNA or RNA molecules that expressone or more alphavirus structural proteins under the direction of apromoter, e.g., the 26S promoter, are used in combination with thehelper molecules of this invention. In one set of RNA moleculeembodiments, the “promoter-assisted helper construct” comprises a firstnucleic acid sequence encoding (i) a 5′ alphavirus replicationrecognition sequence, (ii) a transcriptional promoter, (iii) a nucleicacid sequence encoding one or more alphavirus structural proteins, and(iv) a 3′ alphavirus replication recognition sequence.

In another set of RNA molecule embodiments, the “promoter-assistedhelper construct” is a recombinant helper nucleic acid, as described inWO 2004/085660 (published Oct. 7, 2004 and incorporated herein byreference), comprising: a nucleic acid sequence encoding a 5′ alphavirusreplication recognition sequence, an alphavirus subgenomic promoterimmediately upstream of an IRES element, at least one nucleic acidencoding an alphavirus structural protein, and a nucleic acid encoding a3′ alphavirus replication recognition sequence. In further embodiments,these promoter-assisted helper constructs can comprise a spacer nucleicacid located immediately downstream of the subgenomic promoter andimmediately upstream of the IRES element. The spacer nucleic acid cancomprise or consist of any random or specific non-coding nucleic acidsequence that is of a length sufficient to prevent at least some, and insome embodiments, all translation from the 5′ cap of a messenger RNA,such that translation of the structural proteins is then directed by theIRES, in part or in whole. Alternatively, the spacer nucleic acid can beof a length and sequence structure that imparts sufficient secondarystructure to the nucleic acid to prevent at least some and possibly alltranslation activity from the 5′ cap of a messenger RNA. Thepromoter-assisted helper constructs used in this invention can also beDNA molecules, which can be stably integrated into the genome of thehelper cell or transiently expressed from an episome (e.g., a plasmid)without significant integration. The DNA molecule of this invention canbe any DNA vector, including but not limited to, a non-integrating DNAvector, such as a plasmid, or a viral vector.

In embodiments of this invention employing “helper cells” or “packagingcells” as described herein, and comprising a promoterless RNA moleculeof this invention, the helper cell can further comprise apromoter-assisted helper construct (RNA and/or DNA) in any combinationsuch that the helper cell comprises a combination of nucleotidesequences encoding alphavirus structural proteins sufficient to producean alphavirus replicon particle of this invention. In certainembodiments, the E1 and E2 glycoproteins are encoded by a first helperconstruct, and the capsid protein is encoded by a second helperconstruct. In another embodiment, the E1 glycoprotein, E2 glycoprotein,and capsid protein are each encoded by separate (e.g., first, second andthird) helper constructs. In yet other embodiments, the capsid proteinand either glycoprotein E1 or E2 are encoded by a first helperconstruct, and the remaining glycoprotein E1 or E2 not included in thefirst helper construct is encoded by a second helper construct, with orwithout the capsid coding sequence. In additional embodiments,alphavirus glycoproteins E1 and E2, as well as capsid protein can all beencoded on one helper construct, in any order and/or in anymultiplicity. Among the embodiments included in this invention, it isalso possible that a given alphavirus structural protein is expressed bymore than one helper construct. The promoterless RNA helpers of thisinvention, optionally in combination with other known helpers asdescribed herein, can be introduced into an alphavirus-permissive cellin any combination, in any order and/or in any multiplicity.

In some embodiments of this invention (e.g., for DNA constructs encodingpromoterless RNA molecules or promoter-assisted RNA helper constructs),a promoter for directing transcription of RNA from DNA, i.e., a DNAdependent RNA polymerase is utilized to synthesize RNA in an in vitrotranscription reaction, and specific promoters suitable for this useinclude, but are not limited to, the SP6, T7, and T3 RNA polymerasepromoters.

In all of the embodiments of this invention, it is contemplated that atleast one of the alphavirus structural and/or non-structural proteinsencoded by the promoterless helper molecules and/or promoter-assistedhelper constructs and/or the replicon vector, as well as thenontranslated regions of the replicon nucleic acid, can contain one ormore attenuating mutations, as described herein, in any combination.

The present invention further provides a population of alphavirusreplicon particles, wherein the population contains fewer than onereplication-competent alphavirus particle per 10⁸ alphavirus repliconparticles. In further embodiments, the population contains fewer thanone replication-competent alphavirus particle per 10⁹, 10¹⁰, 10¹¹, 10¹²or 10¹³ alphavirus replicon particles. The present inventionadditionally provides a population of alphavirus replicon particles,wherein the population contains no detectable replication-competentvirus particles, as determined by passage on permissive cells in cultureaccording to methods well known in the art.

Also provided herein is a population of alphavirus replicon particles,wherein the population contains no detectable or fewer than onereplication-competent alphavirus particle per 10⁸, 10⁹, 10¹⁰, 10¹¹, 10¹²or 10¹³ alphavirus replicon particles, as determined by passage onpermissive cells in culture, wherein the alphavirus replicon particlescomprise one or more attenuating mutations in either an alphavirusstructural protein or an alphavirus nonstructural protein or both analphavirus structural protein and an alphavirus nonstructural protein.Additionally provided is a population of alphavirus replicon particles,wherein the population contains no detectable replication-competentvirus particles, as determined by passage on permissive cells inculture, wherein the alphavirus replicon particles comprise one or moreattenuating mutations in either an alphavirus structural protein or analphavirus nonstructural protein or both an alphavirus structuralprotein and an alphavirus nonstructural protein.

It has been confirmed by the inventors that, despite the lack of anidentifiable “packaging signal,” helper RNAs of this invention, as wellas helper RNAs described in the literature, are packaged by thealphavirus structural proteins in the cultured cells, sometimes at afrequency that is considerably higher than that reported in theliterature. Thus, the population of alphavirus replicon particles ofthis invention is distinguished from those particles described in theliterature by the presence of a subset of particles in the population inwhich are packaged the novel helper molecules of this invention.

The terms “alphavirus replicon particles,” “ARPs,” “virus repliconparticles” or “recombinant alphavirus particles,” used interchangeablyherein, mean a virion-like structural complex incorporating analphavirus replicon RNA that expresses one or more heterologous RNAsequences. Typically, the virion-like structural complex includes one ormore alphavirus structural proteins embedded in a lipid envelopeenclosing a nucleocapsid that in turn encloses the RNA. The lipidenvelope is typically derived from the plasma membrane of the cell inwhich the particles are produced. In certain embodiments, the alphavirusreplicon RNA is surrounded by a nucleocapsid structure comprised of thealphavirus capsid protein, and the alphavirus glycoproteins are embeddedin the cell-derived lipid envelope. The structural proteins and repliconRNA may be derived from the same or different alphaviruses. In aspecific embodiment, the replicon RNA is derived from VEE and thestructural proteins are derived from Sindbis virus (see, e.g., Dubenskyet al., U.S. Pat. No. 6,376,236). The alphavirus replicon particles areinfectious but propagation-defective, i.e., the replicon RNA cannotpropagate beyond the host cell that the particles initially infect, inthe absence of the helper nucleic acid(s) encoding the alphavirusstructural proteins.

The terms “alphavirus RNA replicon,” “alphavirus replicon RNA,”alphavirus RNA vector replicon,” and “vector replicon RNA” are usedinterchangeably to refer to an RNA molecule expressing nonstructuralprotein genes such that it can direct its own replication(amplification) and comprises, at a minimum, 5′ and 3′ alphavirusreplication recognition sequences (which may be the minimal sequences,as defined above, but may alternatively be the entire regions from thealphavirus), coding sequences for alphavirus nonstructural proteins, anda polyadenylation tract. It may additionally contain a promoter and/oran IRES. It may also be engineered to express alphavirus structuralproteins. Johnston et al. and Polo et al. describe numerous constructsfor such alphavirus RNA replicons, and such constructs are incorporatedherein by reference. In one embodiment of the alphavirus replicon RNA,the alphavirus nonstructural proteins are separated into two separatetranslational units, as described in U.S. Patent Publication2003-0119182-A1, incorporated herein by reference.

An alphavirus replicon RNA with no heterologous sequences, i.e., anempty replicon, can be used in an alphavirus replicon particle toproduce an adjuvant composition. Alternatively, the alphavirus repliconRNA can express nucleic acid encoding alphavirus structural proteinsand/or other heterologous nucleic acid sequences, the latter of whichcan be chosen from a wide variety of sequences derived from viruses,prokaryotes and/or eukaryotes. Examples of categories of heterologoussequences include, but are not limited to, immunogens (including native,modified or synthetic antigenic proteins, peptides, immunogenicfragments, or epitopes), cytokines, toxins, therapeutic proteins,enzymes, antisense sequences, and immune response modulators. Ifappropriate and desired for the particular application, the transcribedmRNA is then translated, i.e., protein is synthesized or a functionalRNA is produced. These mRNAs are “capped” within the eukaryotic cell,i.e., a methyl-7-guanosine (5′)pppN structure is present at the 5′ endof the mRNA (the “cap” or “5′ cap”), and this cap is recognized by thetranslation initiation factors that synthesize protein from the mRNA.Thus, the 26S promoter directs transcription, and the “cap” provides theinitiation signal for translation.

In some embodiments, the replicon RNA can lack nucleic acid encoding anyalphavirus structural protein(s). In other embodiments, the alphavirusreplicon RNA can comprise nucleic acid encoding one or two alphavirusstructural proteins, but the replicon RNA does not contain nucleic acidencoding all of the alphavirus structural proteins. Thus, the resultingalphavirus replicon particles of this invention arepropagation-defective inasmuch as the replicon RNA does not encode allof the structural proteins required for encapsidation of the repliconRNA and assembly of an infectious virion.

Specific embodiments of the alphavirus RNA replicons utilized in theclaimed invention can contain one or more attenuating mutations asdescribed in detail herein, Examples of an attenuating nucleotidesubstitution include the mutation at nucleotide 3 in the VEE 5′ enddescribed herein and a mutation at nsP1 amino acid position 538, nsP2amino acid position 96, or nsP2 amino acid position 372 in thealphavirus S.A.AR86.

The alphavirus replicon particles of this invention can comprisereplicon RNA from any alphavirus. Furthermore, the alphavirus repliconparticles of this invention can comprise alphavirus structural proteinsfrom any of the alphaviruses of this invention. Thus, the repliconparticles can be made up of replicon RNA and structural proteins fromthe same alphavirus or from different alphaviruses, the latter of whichwould be chimeric alphavirus replicon particles (e.g., a particlecomprising VEE virus-based replicon RNA and Sindbis virus structuralproteins).

In particular embodiments of the present invention, the alphavirusstructural protein of this invention can be a Sindbis virus structuralprotein, a SFV structural protein, a VEE structural protein, a RossRiver virus structural protein, an EEE structural protein and/or a WEEstructural protein. These can be present in any combination with oneanother and can be present in combination with nonstructural proteinsand other alphaviral sequences, such as the 5′ alphavirus replicationrecognition sequence, the alphavirus subgenomic promoter and the 3′alphavirus replication recognition sequence, from any of these or otheralphaviruses, to produce chimeric recombinant alphavirus repliconparticles and/or chimeric recombinant nucleic acids of this invention.

In some embodiments of this invention, the present invention can includealphavirus nucleic acids, alphavirus proteins, alphavirus replicon RNAand/or alphavirus replicon particles including one or more attenuatingmutations, an attenuating mutation being defined as a nucleotidedeletion, addition, and/or substitution of one or more nucleotide(s), ora mutation that comprises rearrangement or chimeric construction, whichresults in a loss of virulence in a live virus containing the mutationas compared to the appropriate wild-type alphavirus.

Appropriate attenuating mutations will be dependent upon the alphavirusused, and will be known to those skilled in the art. Exemplaryattenuating mutations include, but are not limited to, those describedin U.S. Pat. No. 5,505,947 to Johnston et al., U.S. Pat. No. 5,185,440to Johnston et al., U.S. Pat. No. 5,643,576 to Davis et al., U.S. Pat.Nos. 5,792,462; 6,156,558 and 5,639,650 to Johnston et al., thedisclosures of each of which are incorporated herein in their entiretiesby reference.

Specific attenuating mutations for the VEE E1 glycoprotein can includean attenuating mutation at any one of E1 amino acid positions 81, 272 or253. Alphavirus replicon particles made from the VEE-3042 mutant containan isoleucine substitution at E1-81, and virus replicon particles madefrom the VEE-3040 mutant contain an attenuating mutation at E1-253.Specific attenuating mutations for the VEE E2 glycoprotein can includean attenuating mutation at any one of E2 amino acid positions 76, 120,or 209. Alphavirus replicon particles made from the VEE-3014 mutantcontain attenuating mutations at both E1-272 and at E2-209 (see U.S.Pat. No. 5,792,492). A specific attenuating mutation for the VEE E3glycoprotein includes an attenuating mutation consisting of a deletionof E3 amino acids 56-59. Virus replicon particles made from the VEE-3526mutant contain this deletion in E3 (aa56-59) as well as a secondattenuating mutation at E1-253. Specific attenuating mutations for theS.A.AR86E2 glycoprotein include an attenuating mutation at any one of E2amino acid positions 304, 314, 372, or 376. Alternatively, theattenuating mutation can be a substitution, deletion or insertion of anamino acid in the E2 glycoprotein, for example, at any one or more ofthe following amino acid positions in any combination: 158, 159, 160,161 and 162 (see Polo et al., PCT Publication No. WO 00/61772).Alternatively, the RNA molecules of this invention can be derived fromTC83, a vaccine strain of VEE (see WO 2005/113782, which is incorporatedherein by reference).

Another attenuating mutation of this invention can be an attenuatingmutation at nucleotide 3 of the VEE genomic RNA, i.e., the thirdnucleotide following the 5′ methylated cap (see, e.g., U.S. Pat. No.5,643,576 describing a G→C mutation at nt 3). This mutation, located ina non-coding sequence of the virus or replicon, can be a G→A or a G→Umutation in some embodiments. When the alphavirus structural and/ornon-structural proteins are from S.A.AR86, exemplary attenuatingmutations in the structural and non-structural proteins have beendescribed in the literature (see, e.g., U.S. Pat. No. 5,639,650 and U.S.Pat. No. 6,982,087, the disclosures of which are incorporated herein intheir entirety by reference).

The alphavirus of this invention can be a Sindbis virus strain (e.g.,TR339), VEE (e.g., having a mutation at nucleotide 3 of the genomic RNAfollowing the methylated cap or TC83), S.A.AR86 virus, Girdwood S.A.virus, Ockelbo virus, and/or chimeric viruses thereof. The completegenomic sequences, as well as the sequences of the various structuraland non-structural proteins are available in the literature for numerousalphaviruses and include: Sindbis virus genomic sequence (GenBankAccession Nos. J02363, NCBI Accession No. NC_(—)001547), S.A.AR86genomic sequence (GenBank Accession No. U38305), VEE genomic sequence(GenBank Accession No. L04653, NCBI Accession No. NC_(—)001449), TC-83vaccine strain of VEE (Kinney R M et al. (1989) Virology 170:19-30; withcorrection noted in Kinney R M et al. (1993) J. Virol. 67(3):1269-1277);Girdwood S. A genomic sequence (GenBank Accession No. U38304), SemlikiForest virus genomic sequence (GenBank Accession No. X04129, NCBIAccession No. NC_(—)003215), and the TR339 genomic sequence (Klimstra etal., (1988) J. Virol. 72:7357; McKnight et al. (1996) J. Virol.70:1981).

Alphavirus replicon particles are prepared according to the methodsdisclosed herein in combination with techniques known to those skilledin the art. The methods include first introducing the selected helper(s)and an alphavirus replicon RNA into a population ofalphavirus-permissive cells, and then incubating the cells underconditions well known in the art that allow for the production ofalphavirus replicon particles. The step of introducing the helper(s) andalphavirus replicon RNA into the population of helper cells can beperformed by any suitable means, as disclosed herein and as known tothose generally skilled in the art.

Populations of alphavirus replicon particles are collected from thehelper or packaging cells according to methods, e.g., as described inU.S. Pat. No. 7,078,218, the content of which is incorporated herein byreference in its entirety. Alternatively, they can be collected frompackaging cells using other techniques known to those skilled in the art(e.g., U.S. Pat. Nos. 5,492,462 and 6,156,558). These populations areevaluated for the presence of replication competent virus (RCV)according to methods as described herein and as known in the literature.The populations of this invention contain no detectable RCV, asdetermined by passage on alphavirus-permissive cells in culture.

In some embodiments, the present invention can be employed to package analphavirus RNA replicon encoding an immunogenic polypeptide in a subject(e.g., for vaccination), for immunotherapy (e.g., to treat a subjectwith cancer or tumors), or an immunomodulatory factor (e.g., foradjuvanting ARPs or other vaccine modalities). The present inventionprovides methods of eliciting or enhancing an immune response in asubject, comprising administering to the subject an effective amount ofa nucleic acid packaged into particles by the helper constructs of thisinvention

As used herein, “eliciting an immune response” and “immunizing asubject” includes the development, in a subject, of a humoral and/or acellular immune response to a protein and/or polypeptide of thisinvention (e.g., an immunogen, an antigen, an immunogenic peptide,and/or one or more epitopes). A “humoral” immune response, as this termis well known in the art, refers to an immune response comprisingantibodies, while a “cellular” immune response, as this term is wellknown in the art, refers to an immune response comprising T-lymphocytesand other white blood cells, especially the immunogen-specific responseby HLA-restricted cytolytic T-cells, i.e., “CTLs.”

It is also contemplated that the nucleic acids, particles, populationsand pharmaceutical compositions of this invention can be employed inmethods of delivering a NOT of interest to a cell, which can be a cellin a subject. Thus, the present invention provides a method ofdelivering a heterologous nucleic acid to a cell, comprising introducinginto the cell an effective amount of a particle, population and/orcomposition packaged with the helper constructs of this invention. Alsoprovided is a method of delivering a heterologous nucleic acid to a cellin a subject, comprising delivering to the subject an effective amountof a particle, population and/or composition packaged with the helperconstructs of this invention. The cell can be any cell that can take upand express exogenous nucleic acids. The cell is maintained underconditions whereby the heterologous nucleic acid is expressed to producea protein, peptide or other coding sequence product (e.g., a functionalRNA sequence) encoded by the heterologous nucleic acid. Such methods canbe employed to impart a therapeutic effect on a cell and/or a subject ofthis invention, according to well known protocols for immunizationand/or gene therapy.

A “subject” of this invention includes, but is not limited to,warm-blooded animals, e.g., humans, non-human primates, horses, cows,cats, dogs, pigs, rats, and mice.

The present invention further provides a composition (e.g., apharmaceutical composition) comprising a particle and/or population ofparticles of this invention in a pharmaceutically acceptable carrier. By“pharmaceutically acceptable” is meant a material that is notbiologically or otherwise undesirable, i.e., the material may beadministered to a subject along with the selected particles, and/orpopulations thereof, without causing substantial deleterious biologicaleffects or interacting in a deleterious manner with any of the othercomponents of the composition in which it is contained. Thepharmaceutically acceptable carrier is suitable for administration ordelivery to humans and other subjects of this invention. The carrierwould naturally be selected to minimize any degradation of the activeingredient and to minimize any adverse side effects in the subject, aswould be well known to one of skill in the art (see, e.g., Remington'sPharmaceutical Science; latest edition). Pharmaceutical formulations,such as vaccines or other immunogenic compositions, of the presentinvention comprise an immunogenic amount of the infectious, propagationdefective alphavirus replicon particles produced using the helperconstructs of this invention, in combination with a pharmaceuticallyacceptable carrier. Exemplary pharmaceutically acceptable carriersinclude, but are not limited to, sterile pyrogen-free water and sterilepyrogen-free physiological saline solution.

An “immunogenic amount” is an amount of the infectious alphavirusparticles in the populations of this invention that is sufficient toevoke an immune response in a subject to which the population ofparticles is administered or delivered. An amount of from about 10⁴ toabout 10⁹, especially 10⁶ to 10⁸, infectious units, or “IU”, asdetermined by assays described herein, per dose is considered suitable,depending upon the age and species of the subject being treated.Administration may be by any suitable means, such as intraperitoneally,intramuscularly, intranasally, intravaginally, intravenously,intradermally (e.g., by a gene gun), intrarectally and/orsubcutaneously. The compositions herein may be administered via a skinscarification method, and/or transdermally via a patch or liquid. Thecompositions can be delivered subdermally in the form of a biodegradablematerial that releases the compositions over a period of time.

As used herein, “effective amount” refers to an amount of a populationor composition or formulation of this invention that is sufficient toproduce a desired effect, which can be a therapeutic effect. Theeffective amount will vary with the age, general condition of thesubject, the severity of the condition being treated, the particularagent administered, the duration of the treatment, the nature of anyconcurrent treatment, the pharmaceutically acceptable carrier used, andlike factors within the knowledge and expertise of those skilled in theart. As appropriate, an “effective amount” in any individual case can bedetermined by one of ordinary skill in the art by reference to thepertinent texts and literature and/or by using routine experimentation.(See, for example, Remington, The Science And Practice of Pharmacy (20thed. 2000)).

Alternatively, pharmaceutical formulations of the present invention maybe suitable for administration to the mucous membranes of a subject(e.g., via intranasal administration, buccal administration and/orinhalation). The formulations may be conveniently prepared in unitdosage form and may be prepared by any of the methods well known in theart.

Also, the composition of this invention may be used to infect or betransfected into dendritic cells, which are isolated or grown from asubject's cells, according to methods well known in the art, or ontobulk peripheral blood mononuclear cells (PBMC) or various cellsubtractions thereof from a subject.

If ex vivo methods are employed, cells or tissues can be removed andmaintained outside the body according to standard protocols well knownin the art while the compositions of this invention are introduced intothe cells or tissues.

Immunogenic compositions comprising a population of the particles (whichdirect the expression of the nucleic acid sequence(s) of interest whenthe compositions are administered to a human or animal) of the presentinvention may be formulated by any means known in the art. Suchcompositions, especially vaccines, are typically prepared asinjectables, either as liquid solutions or suspensions. Solid formssuitable for solution in, or suspension in, liquid prior to injectionmay also be prepared. Lyophilized preparations are also suitable.

The active immunogenic ingredients (e.g., the alphavirus repliconparticles) are often mixed with excipients and/or carriers that arepharmaceutically acceptable and/or compatible with the activeingredient. Suitable excipients include but are not limited to sterilewater, saline, dextrose, glycerol, ethanol, or the like and combinationsthereof, as well as stabilizers, e.g., HSA or other suitable proteinsand reducing sugars.

In addition, if desired, the vaccines may contain minor amounts ofauxiliary substances such as wetting and/or emulsifying agents, pHbuffering agents, and/or adjuvants that enhance the effectiveness of thevaccine. Examples of adjuvants which may be effective include but arenot limited to: QS-21, Freund's adjuvant (complete and incomplete),aluminum salts (alum), aluminum phosphate, aluminum hydroxide;N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP);N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to asnor-MDP);N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3hydroxyphosphoryloxy)-ethylamine(CGP 19835A, referred to as MTP-PE); and RIBI, which contains threecomponents extracted from bacteria, monophosphoryl lipid A, trehalosedimycolate and cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween80 emulsion.

Additional examples of adjuvants can include, but are not limited to,oil-in-water emulsion formulations, immunostimulating agents, such asbacterial cell wall components or synthetic molecules, oroligonucleotides (e.g., CpGs) and nucleic acid polymers (both doublestranded and single stranded RNA and DNA), which can incorporatealternative backbone moieties, e.g., polyvinyl polymers.

The effectiveness of an adjuvant may be determined by measuring theamount of antibodies or cytotoxic T-cells directed against theimmunogenic product of the alphavirus replicon particles resulting fromadministration of the particle-containing composition in a vaccineformulation that also comprises an adjuvant or combination of adjuvants.Such additional formulations and modes of administration as are known inthe art may also be used.

Adjuvants can be combined, either with the compositions of thisinvention or with other vaccine formulations that can be used incombination with the compositions of this invention.

The compositions of the present invention can also include othermedicinal agents, pharmaceutical agents, carriers, and diluents.

The compositions of this invention can be optimized and combined withother vaccination regimens to provide the broadest (i.e., covering allaspects of the immune response, including those features describedhereinabove) cellular and humoral responses possible. In certainembodiments, this can include the use of heterologous prime-booststrategies, in which the compositions of this invention are used incombination with a composition comprising one or more of the following:immunogens derived from a pathogen or tumor, recombinant immunogens,naked nucleic acids, nucleic acids formulated with lipid-containingmoieties, non-alphavirus vectors (including but not limited to poxvectors, adenoviral vectors, adeno-associated viral vectors, herpesvirus vectors, vesicular stomatitis virus vectors, paramyxoviralvectors, parvovirus vectors, papovavirus vectors, retroviral vectors,lentivirus vectors), and other alphavirus vectors. The viral vectors canbe virus-like particles or nucleic acids. Exemplary alphavirus vectorscan be replicon-containing particles, DNA-based replicon-containingvectors (sometimes referred to as an “ELVIS” system, see, for example,U.S. Pat. No. 5,814,482) and/or naked RNA vectors.

The immunogenic (or otherwise biologically active) alphavirusparticle-containing populations and compositions of this invention areadministered in a manner compatible with the dosage formulation, and insuch amount as will be prophylactically and/or therapeuticallyeffective. The quantity to be administered, which is generally in therange of about 10⁴ to about 10⁹ infectious units per mL in a dose,depends on the subject to be treated, the route by which the particlesare administered or delivered, the immunogenicity of the expressionproduct, the types of effector immune responses desired, and the degreeof protection desired. In some embodiments, doses of about 10⁶, 10⁷, and10⁸ I.U. may be particularly effective in human subjects. Effectiveamounts of the active ingredient required to be administered ordelivered may depend on the judgment of the physician, veterinarian orother health practitioner and may be specific for a given subject, butsuch a determination is within the skill of such a practitioner.

The compositions and formulations of this invention may be given in asingle dose or multiple dose schedule. A multiple dose schedule is onein which a primary course of administration may include 1 to 10 or moreseparate doses, followed by other doses administered at subsequent timeintervals as required to maintain and or reinforce the desired effect(e.g., an immune response), e.g., weekly or at 1 to 4 months for asecond dose, and if needed, a subsequent dose(s) after several months(e.g., 4 or 6 months)/years.

Efficacy of the treatment methods of this invention can be determinedaccording to well known protocols for determining the outcome of atreatment of a disorder of this invention. Determinants of efficacy oftreatment, include, but are not limited to, overall survival,disease-free survival, improvement in symptoms, time to progressionand/or quality of life, etc., as are well known in the art.

“Treat” or “treating” or “treatment” refers to any type of action thatimparts a modulating effect, which, for example, can be a beneficialeffect, to a subject afflicted with a disorder, disease or illness,including improvement in the condition of the subject (e.g., in one ormore symptoms), delay or reduction in the progression of the condition,prevention or delay of the onset of the disorder, disease or illness,and/or change in any of the clinical parameters of a disorder, diseaseor illness, etc., as would be well known in the art.

It is understood that the foregoing detailed description is given merelyby way of illustration and that modifications and variations may be madetherein without departing from the spirit and scope of the invention.

EXAMPLES Example 1 Construction of dHcap and dHgp Helpers

Primers were designed (capsid F (SEQ ID NO:98), GP F (SEQ ID NO:60) and13-101.pr4 (SEQ ID NO:61) (Table 1), to amplify the capsid andglycoprotein (GP) genes out of the VEE helper plasmids (referred to as“13.2.2” for the capsid helper and “13.4.6” for the glycoproteinhelper), which are described in U.S. Pat. Nos. 5,792,462, Pushko et al.,1997 (Virology 239:389-401), and PCT publication WO 02/03917 (Olmsted etal.). These primers provide an Rsr II restriction site and also bind tothe start of the capsid or glycoprotein coding sequence, respectively.The DNA plasmids described in the above-cited references are aconvenient source for obtaining the structural protein coding fragments,e.g., by PCR amplification. Alternatively, these coding fragments can beobtained from full-length clones of VEE or attenuated variants thereof(see U.S. Pat. No. 5,185,440; U.S. Pat. No. 5,505,947).

Amplification with these primers resulted in fragments with thefollowing elements, listed from the 5′ to the 3′ ends of the PCRproduct: 5′-RsrII restriction site, VEE structural protein codingsequence ORF, 3′ UTR, SphI restriction site −3′. The PCR products werethen digested with RsrII and SphI restriction enzymes and ligated intoan empty VEE replicon vector, as described in U.S. Pat. No. 5,792,462,Pushko et al., 1997 (Virology 239:389-401) and PCT Publication No. WO02/03917 (Olmsted et al.). This replicon RNA contains the VEEnonstructural genes and a single copy of the 26S subgenomic RNA promoterfollowed by a multiple cloning site (MCS). In a vaccine construct, oneor more coding sequences encoding an immunogen are inserted into thiscloning site. This vector is digested with RsrII and SphI (removing mostof nsP1 and all of nsPs2-4), and upon ligation, helpers are generatedwhich comprise the complete alphavirus 5′ and 3′ ends, i.e.,“full-length” ends. These two helpers are therefore designated dHcap(FL)and dHgp(FL) and they have the 5′ sequences of SEQ ID NO:1 and SEQ IDNO:10, respectively and the 3′ sequences of SEQ ID NO:55 and SEQ IDNO:56, respectively (FIG. 1).

Subsequently, eight consecutive deletions of approximately 50 nt eachwere made in the 522 nt 5′ end present in both the dHcap(FL) anddHgp(FL) helpers (FIG. 2). The procedure was carried out in two steps.First, eight different reverse primers (dHelp1-8 R, SEQ ID NOS: 63-70)were designed complementary to the 5′ end up to position 502 of the13.2.2 and 13.4.6 helpers (described hereinabove), and each wasengineered to additionally contain an RsrII restriction site (Table 1).A forward primer (3-16.1.1 (SEQ ID NO:62), Table 1) was designed, whichwhen combined with any of the reverse primers, amplified a fragment withthe following elements (listed 5′ to 3′): 5′-XbaI restriction site, T7promoter, 5′ truncated end, RsrII restriction site-3′. Second, theamplified 5′ truncated end fragments were cloned into the dHcap(FL) anddHgp(FL) helpers linearized with XbaI and RsrII. This generated eightsets of 5′ truncated end helper constructs, designated dHcap1-8 anddHgp1-8, which have the 5′sequences of SEQ ID NOS: 2-9 and SEQ ID NOS:11-18, respectively. The 3′ sequence of each member of the dHcap seriesis provided herein as SEQ ID NO:55 and the 3′ sequence of each member ofthe dHgp series is provided herein as SEQ ID NO:56.

Example 2 Methods for Expression Analysis of Promoterless HelperExpression Cassettes

To determine how well the Δ26S helper configurations described hereinexpressed VEE structural proteins, each helper was electroporated intoVero cells along with a VEE replicon vector as described above. Forpurposes of demonstrating the capability of the novel promoterlessstructural protein expression cassettes of this invention, VEE repliconswere constructed by inserting a GFP or a botulinum neurotoxin codingsequence into the VEE replicon vector's cloning site. Expression ofthese coding sequences from particles made with various combinations ofthe promoterless structural protein expression cassettes describedherein demonstrated the utility and novelty of these cassettes.

RNA was transcribed from each helper and replicon vector by run-offtranscription using RiboMAX T7 Express® transcription kits (PromegaCorporation, Madison, Wis.) according to the manufacturer's procedure.Before electroporation, helper and replicon RNAs were purified bysilica-based chromatography. Thirty micrograms (30 μg) of each helperand replicon RNA were combined and electroporated into 3-5×10⁷ Verocells. Electroporated cells were diluted in medium and seeded into 25cm² flasks or 96 well plates. The electroporated cells were thenincubated for 16-24 hr at 37° C.

A. IFA Analysis

Electroporated cells seeded into 96 well plates were washed withphosphate buffered saline (PBS) one time and then fixed withacetone:methanol (1:1) at room temperature for five min. The cells werethen analyzed for expression of VEE capsid or GP protein usingstructural protein specific mouse antibodies. Primary antibody wasdiluted in PBS:FBS (1:1) and 100 μl was added to each well. Plates wereincubated at 37° C. for 30 min, washed with 150 μl PBS three times andthen incubated with Alexa Fluor 488 goat anti-mouse secondary antibody(Invitrogen, Carlsbad, Calif.) for 30 min at 37° C. After incubation,cells were washed again as described above and a final volume of 100 μlPBS was added to each well before inspection by ultraviolet fluorescencemicroscopy (Nikon Eclipse TE300).

B. Northern Analysis

Electroporated cells seeded into 25 cm² flasks were washed with PBS andthen total cellular RNA was extracted using RNAwiz RNA® isolationreagent (Ambion, Austin, Tex.) following the manufacturer's suggestedprotocol. RNA concentration was determined by spectrophotometry. Fivemicrograms (5 μg) of each sample were electrophoresed through a 1%glyoxal agarose gel and RNA was passively transferred to BrightStarPlus® (Ambion) membranes. Northern analysis was carried out with abiotinylated DNA oligo specific for the positive strand of the VEE 3′replication recognition sequence using a BrightStar BioDetec® kit(Ambion) following the manufacturer's suggested protocol.Chemiluminescence was detected by exposing the processed membranes tofilm.

C. Analysis of dHcap(FL) and dHgp(FL) Expression

To demonstrate that the full-length Δ26S helpers (dHcap(FL) anddHgp(FL)) could be replicated and express proteins, these helper RNAswere electroporated into cells along with a replicon vector, which isneeded to provide the alphavirus non-structural proteins that facilitatereplication of the helper RNAs. Vero cells were electroporated witheither 30 or 60 μg of dHcap(FL) or dHgp(FL) helper RNA combined with 30μg of replicon RNA. The electroporated cells were processed for IFA,Western blot and Northern analysis as described above.

Example 3 Expression Analysis for Full-Length and Truncated Δ26S Helpers

The dHcap(FL) and dHgp(FL) helpers expressed protein as determined byIFA and Western blot and were replicated efficiently as demonstrated byNorthern blot.

The complete set of truncated Δ26S helpers (deletions 1-8) for bothcapsid and GP were analyzed for protein expression by IFA and byNorthern blot to determine how well each was expressed and replicated.Each dHcap helper RNA was combined with a VEE replicon RNA and the13.4.6 glycoprotein helper RNA, and the three RNAs were electroporatedinto Vero cells. Northern analysis and IFA were carried out as describedabove. The results of IFA using a capsid specific antibody are shown inTable 2. All dHcap helpers were positive for capsid expression by IFAalthough the dHcap8 helper was only weakly positive.

Northern analysis of RNA extracted from electroporated cells indicatedthat all of the truncated capsid Δ26S helpers replicated well except fordHcap8.

The dHgp helpers were examined in a similar manner but the 13.2.2 capsidhelper was not included in this experiment. Each dHgp helper wascombined with a VEE replicon RNA, electroporated into cells, and sampleswere generated as described above for IFA and Northern analysis. Resultsof anti-GP IFA are shown in Table 3. Similar to the dHcap helpers, alldHgp helpers were positive except dHgp8. All dHgp helpers replicatedwell with the exception of dHgp8.

Example 4 Modified Promoterless Helper Constructs

The inventors noted that the dHcap(FL) and dHgp(FL) helpers expressedfusion proteins, as revealed by Western blotting. Such fusion proteinscould be the result of initiation of translation at in-frame startcodons upstream of the start codon for capsid or GP on the Δ26S helpertranscripts. One such upstream codon is the native start codon for VEEnsP1 (located at nucleotide 45 in the VEE viral genome), which ispresent in the 5′ end of both the dHcap and dHgp helpers, and is in afavorable context for initiation of translation (e.g., a Kozak consensussequence). It is possible that a start codon in a favorable Kozakenvironment could be used by ribosomes scanning from the capped 5′ endof these helpers, thereby generating fusion proteins that are notfunctional and decreasing the production of functional capsid andglycoprotein polypeptides from the appropriate start codon locatedfurther downstream.

Two approaches were used to decrease the amount of such fusion proteinsproduced and increase full-length capsid and glycoprotein proteinexpression. First, the favorable start codon described above was mutatedto a TAG stop codon and the remaining start codons were left unchanged.This approach was taken to keep the 5′ end sequence as close to thesequence present in the native VEE genome as possible, in order tomaintain the replication elements relied upon for these helpers. Second,all of the start codons downstream of nt 3 (including the nsP1(favorable) start codon) and the capsid or glycoprotein coding sequenceopen reading frame (ORF) were changed from AUG to GUG (there were atotal of 12 such changes). This approach was taken to determine whetherless favorable ATG codons (AUG in RNA) might also have detrimentaleffects on the production of full-length capsid or glycoproteinexpression.

A. Construction of dHcap-mut1 and dHgp-mut1 Helpers

To generate dHcap and dHgp helpers that have the favorable nsP1 startcodon changed to a TAG stop codon, site directed mutagenesis was carriedout on each dHcap and dHgp helper, generating a complete set (FL andtruncations 1-7) of mutated helpers, designated dHcap-mut1 and dHgp-mut1helpers, which have 5′ sequences as provided herein as SEQ ID NOS: 35-42and 43-50, respectively. Site directed mutagenesis was carried out witha Quikchange XL® site directed mutagenesis kit (Stratagene, La Jolla,Calif.) according to the manufacturer's protocol using forward (SEQ IDNO:71) and reverse (SEQ ID NO:72) primers in Table 4.

B. Construction of dHcap-mm and dHgp-mm Helpers

To generate dHcap and dHgp helpers with 5′ ends that do not have anystart codons downstream of nt 3 and the capsid or GP ORF start codons,site directed mutagenesis was carried out to change all intervening ATG(AUG IN RNA) codons to GTG (GUG in RNA) codons. The dHgp(FL) constructwas used as the template for site directed mutagenesis. A Quikchange®multi site-directed mutagenesis kit (Stratagene) was used to introducethe codon changes using the manufacturer's protocol. The primers used tointroduce the codon changes are shown in Table 5 (SEQ ID NOS: 73-82).The dHgp(FL) construct containing all of the codon changes wasdesignated dHgp(FL)-mm (having the 5′ sequence provided herein as SEQ IDNO: 19). After sequence confirmation that all codon changes werepresent, this DNA was used to generate the dHcap(FL)-mm construct byreplacing the dHcap(FL) 5′ replication recognition sequence with the 5′replication recognition sequence from dHgp(FL)-nm. This was accomplishedby digesting both DNAs with RsrII and Not I enzymes. The dHgp(FL)-mmRsrII/NotI 5′ replication recognition sequence fragment was then ligatedwith the linearized dHcap(FL) DNA, generating dHcap(FL)-mm (having the5′ sequence provided herein as SEQ ID NO:27). In addition, thedHgp(FL)-mm DNA was used as the template to generate the 5′ truncatedend sets for both capsid and GP helpers using the method and primersdescribed above for dHcap1-7 and dHgp1-7. The new helpers weredesignated dHcap1mm-dHcap7 mm (having 5′ sequences provided herein asSEQ ID NOS:20-26) and dHgp1mm-dHgp7 mm (having 5′ sequences providedherein as SEQ ID NOS:28-34).

C. Analysis of Expression of mut1 and mm Promoterless Helpers

Protein production from various mut1 and mm versions of the Δ26S helpersdescribed above was analyzed. In this experiment, the dHcap6-mut1 (withthe 5′ sequence provided herein as SEQ ID NO:41), dHcap6-mm (with the 5′sequence provided herein as SEQ ID NO:25), dHcap7-mm (with the 5′sequence provided herein as SEQ ID NO:26) and dHgp7-mm (with the 5′sequence provided herein as SEQ ID NO:27), as well as the 13.2.2 and13.4.6 helpers, were analyzed by Western blot. The Δ26S helperscontaining the mm mutations expressed primarily full length capsid or GPproteins with little or no fusion proteins detectable. The mut1 helpersexpressed significant amounts of full-length structural protein, butthey also continued to express some fusion proteins.

Northern analysis was carried out on the same samples to analyze thereplication characteristics of the mut1 and mm Δ26S helpers. The resultsindicate that the dHcap6-mut1 helper replicates as well as the 13.2.2capsid helper. In contrast, the dHcap6-mm, dHcap7-mm and dHgp7-mmhelpers appear to replicate to a lesser extent than 13.2.2 or mut1helpers.

Example 5 VEE Replicon Particle Generation with Δ26S Helpers

Listed in Table 6 are a number of experiments combining differentpromoterless capsid and GP helpers with a VEE replicon RNA to produceVEE replicon particles (VRP). In addition, the amount of each helper RNAintroduced into cells was also varied in some experiments. VRPs weregenerated by electroporating 5×10⁷ to 1×10⁸ Vero cells with theindicated amounts of helper RNA as well as 30 μg of replicon RNA. Ingeneral, for all experiments in which particles are generated,electroporated cells were seeded into 300 cm² flasks containing serumfree media and incubated 16-24 hr before the VRPs were harvested.

VRP titers were determined by infecting Vero cells, grown in 96 wellplates, with ten-fold serial dilutions of sample, incubating the cellsfor 16-18 hr, fixing the cells and performing IFA with antibodiesspecific for VEE nsP2 protein or the product of the nucleic acid ofinterest. VRP yields are reported either as total yield from anexperiment (i.e., Table 6) or on a per ml basis from a 20 ml preparation(Tables 7, 9-13, 15 and 16).

These preparations were also tested for the presence ofreplication-competent virus (RCV) by a cytopathic effect (CPE) assay.The CPE assay consisted of two blind passages in cell culture to screenfor the presence of RCV. For Passage 1, samples from a VRP preparationwere incubated with Vero cell monolayers for 1 hr at 37° C., then thesample fluids were removed and replaced with fresh medium, and thecultures were incubated for 24 hr to allow amplification of any RCV thatmight be present. For Passage 2, cell culture supernatants at the end ofPassage 1 were added to fresh Vero cell monolayers and incubated at 37°C. for 72 hr. At the end of Passage 2, cultures were inspected for CPEusing an inverted light microscope. This assay has been standardized andevaluated for sensitivity in detecting viable virus in the presence of alarge excess of VRP. Using either V3014 or TC-83 viruses in this assay,spiking studies revealed a lower limit of detection of 3-8 PFU on abackground of 1×10⁸ VRP. This assay has been performed on more than 10¹³VRPs produced with the promoterless helpers of this invention, and noRCV has ever been detected. Despite the limit of detection of thisassay, theoretical calculations of the possible recombination frequencyfor generation of RCV would be much lower using this limit of detection,i.e., 1 in 10¹⁰, 1 in 10¹¹, 1 in 10¹², or 1 in 10¹³ VRPs.

Example 6 “Split Glycoprotein” Promoterless Helpers

A. Construction of Separate E2 and E1 Promoterless Helpers

Construction of glycoprotein promoterless helpers in which the E2 and E1coding sequences were placed on separate helpers was performed bycloning the E2 and E1 glycoprotein cassettes separately into thebackbone of the dHgp6-mut1 helper. Primers were designed to amplify byPCR the capsid-E3-E2 region of the VEE structural protein coding regionfrom pHCMV-Vsp (see U.S. Pat. No. 7,045,335, incorporated herein byreference). The amplified fragment was cloned into the pCR-Blunt IITOPO® vector (Invitrogen), generating pCR-CE3E2. The CE3E2 cassette wassequenced to ensure that no errors were introduced during PCRamplification. To produce a promoter-assisted helper that contained theCE3E2 structural region, the pCR-CE3E2 DNA was digested with SpeIrestriction enzyme to release an E3E2 fragment. The E3E2 (SpeI) fragmentwas then ligated with the capsid helper (13.2.2) linearized with SpeIenzyme to produce pHCE3E2. The promoterless E2 helper (designateddHE2-6M1) was prepared by digesting the E3-E2 coding region frompHCE3E2. The pHCE3E2 DNA plasmid was first linearized with AscIrestriction enzyme and then treated with T4 DNA polymerase to create ablunt end. Similarly, the dHgp6-mut1 DNA plasmid was linearized withSphI restriction enzyme and T4 DNA polymerase-treated to create a bluntend. Both linearized, T4-polymerase treated DNAs were then digested withSpeI restriction enzyme, and the resulting 3.6 kb dHgp6-mut1 vectorfragment and 1.4 kb E3-E2 fragment were each gel-purified. The twopurified fragments were then ligated together using T4 DNA ligase toproduce the dHE2-6M1 promoterless helper.

Generation of a promoterless E1 helper was accomplished in severalsteps. Primers were designed to amplify two structural protein codingsequence fragments: 1) capsid-E3 (CE3), and 2) 6K-E1 (6KE1). The PCRproducts were cloned into the pCR-Blunt TOPO® vector (Invitrogen),generating pCR-CE3 and pCR-6KE1. The clones were sequenced to ensurethat no errors were introduced during amplification. To produce acassette that contained both the E3 and 6K leader sequences upstream ofthe E1 glycoprotein, another intermediate construct was produced. Thiswas accomplished by digesting pCR-6KE1 DNA with BamHI enzyme andpurifying the 6KE1 fragment. The 6KE1 (BamHI) fragment was then ligatedwith pCR-CE3 DNA linearized with BamHI enzyme, generating pCR-CE36KE1.To generate a promoter-assisted helper containing the CE36KE1 cassette,pCR-CE36KE1 DNA was digested with SpeI and SphI enzymes releasing thestructural protein coding sequence cassette. The CE36KE1 (SpeI/SphI)fragment was then ligated with capsid helper (13.2.2) linearized withSpeI and SphI to produce pHCE36KE1. Generation of the promoterless E1helper (designated dHE1-6M1) was accomplished by digesting the E3-6K-E1coding region from the pHCE36KE1 plasmid. The pHCE36KE1 and dHgp6-mut1DNA plasmids were digested with SpeI and SphI restriction enzymes andthe resulting 3.6 kb dHgp6-mut1 vector fragment and 1.7 kb E3-6K-E1fragments were gel-purified. The two purified fragments were thenligated together using T4 DNA ligase to produce the dHE1-6M1promoterless helper.

B. Analysis of Split Glycoprotein Promoterless Helpers

The individual glycoprotein helpers were transcribed in vitro, and theRNA transcripts were purified prior to being electroporated into Verocells along with a VEE replicon RNA. Helper replication was analyzed byNorthern blot and protein expression was analyzed by IFA using E1 and E2glycoprotein specific antibodies. Northern results indicate the both thedHE1-6M1 and dHE2-6M1 helper replicate efficiently. A representativeNorthern blot is shown in FIG. 3.

To determine whether the two individual glycoprotein-expressingpromoterless helpers could be combined with a Δ26S capsid helper topackage a replicon RNA to produce VRP, the three helpers were combinedwith VEE replicon RNA expressing a botulinum neurotoxin A fragment andelectroporated into Vero cells. VRP yields from one experiment are shownin Table 7.

Example 7 Modified 5′ and 3′ End Promoterless Helper Cassettes

A. Construction of Modified 5′ End Helper Cassettes

The predicted secondary structure at the 5′ end (˜first 250 nt) of theRNA of most alphaviruses contains four stem loop (SL) structures (SL1,SL2, SL3 and SL4). Frolov et. al. (RNA, 7:1638-1651 (2001)) demonstratedthat removal of the nucleotide sequences encoding SL2 from a Sindbisvirus helper RNA increased replication of that helper.

The SL2 region in the VEE 5′ end (based on the M-fold program), nt 46 tont 116 inclusive, was removed from the dHcap6-mut1 by PCR as follows.Two fragments were amplified from dHcap6-mut1 DNA. A 5′ fragment ofapproximately 1 kilobase (kb) was amplified with primers 13-82.1.9 [SEQID NO. 83] and dLS2(EcoRV) R [SEQ ID NO. 84] (Table 8) that containedthe 45 nucleotides at the 5′ end of dHcap6-mut1 and the nucleotidesencoding the backbone plasmid sequence. A 3′ fragment of approximately1.5 kb was amplified with primers dSL2 (EcoRV) F [SEQ ID NO. 85] and3-8.pr4 [SEQ ID NO. 86] (Table 8) that contained the portion of the VEE5′ end beginning with nucleotide 117 and the nucleotides encoding theentire capsid sequence through the VEE 3′ end. The 5′ ˜1 kb PCR fragmentwas digested with XhoI and EcoRV restriction enzymes. The 3′ ˜1.5 kb PCRfragment was digested with EcoRV and NotI restriction enzymes. PlasmiddHgp6-mut1 was linearized by digestion with XhoI and NotI and theresulting ˜2.5 Kb vector backbone was purified. To generate the newhelper in which the SL2 region was deleted, herein referred to as“dHcap6-mut1(dSL2),” the 5′ (XhoI/EcoRV) fragment, 3′ (EcoRV/NotI)fragment, and the XhoI/NotI linearized vector were ligated together. ThedHcap6-mut1(dSL2) helper, with a 5′ end the sequence of which isprovided herein as SEQ ID NO. 51, was completely sequenced to ensurethat no errors were introduced during PCR amplification. To generate thematching dHgp6-mut1(dSL2) helper, dHgp6-mut1 DNA was digested with XhoIand RsrII restriction enzymes and the 5.4 kb fragment was purified. Themodified 5′ end from dHcap6-mut1(dSL2) was collected by digesting thisDNA with XhoI and RsrII and purifying the 1.1 kb fragment. These twofragments were ligated together to generate dHgp6-mut1(dSL2), which hasthe identical 5′ end [SEQ ID NO. 51] as dHcap6-mut1(dSL2).

B. Construction of Shortened 3′-End Promoterless Helper Cassettes.

In these examples, for the capsid helper constructs dHcap(FL), dHcap1through dHcap7, dHcap(FL)mm, dHcap1mm through dHcap7 mm, dHcap(FL)mut1,and dHcap1mut1 through dHcap7mut1, the 3′ end sequence is providedherein as SEQ ID NO. 55. Although the VEE capsid helpers of thisinvention lack the complete glycoprotein coding region, a small portionof the E3 protein remains on the capsid helper to allow thechymotrypsin-like cleavage to occur within the packaging cell to producemature capsid protein. For the glycoprotein helper constructs dHgp(FL),dHgp1 through dHgp7, dHgp(FL)mm, dHgp1mm through dHgp7 mm, dHgp(FL)mut1,and dHgp1mut1 through dHgp7mut1, the 3′ end sequence was a shortersequence, since the sequence comprising the cleavage site for generatingthe mature capsid protein is not required in the glycoprotein helperconstructs. The 3′ sequence used for these glycoprotein constructs inthese examples is provided herein as SEQ ID NO. 56.

In addition, promoterless RNA helpers with shorter 3′ end lengths wereconstructed. By reducing the amount of alphavirus 3′ end sequence, thetheoretical possibility for a second recombination event, which would berequired to generate replication competent VEE virus, is furtherreduced. Initially, a glycoprotein helper with a functional 26S promotercontaining only the 19 nucleotides comprising the alphavirus highlyconserved 3′ sequence [SEQ ID NO. 52] was produced in the following twosteps. First, a plasmid was produced that contained a glycoprotein (GP)coding sequence cassette with unique 5′ and 3′ restriction sites.Primers were designed to amplify the VEE GP with a unique SphI site justafter the E1 termination codon at the 3′ end (“GP (SphI) R,” SEQ ID NO.87, Table 8) and an existing internal SpeI site at the 5′ end(“3-16.1.3,” SEQ ID NO. 88, Table 8). The amplified fragment was TAcloned into pCR2.1 DNA (Invitrogen, Carlsbad, Calif.) generatingpCR2.1/GP 19 nt 5′. Second, a forward primer was designed to introduce aSphI site just upstream of the 19 nucleotide conserved sequence at theVEE 3′ end (3′ trunc (SphI) F, SEQ ID NO. 89, Table 8). A reverseprimer, specific for the plasmid backbone sequence, was designed toamplify a fragment that would contain a unique AflII restriction site atthe 3′ end (3′ trunc (AflIII) R, SEQ ID NO. 90, Table 8). The fragmentresulting from amplification with these primers was digested with SphIand AflII and ligated into the 13.4.6 glycoprotein helper (described inExample 1), which had been linearized with SphI and AflII restrictionenzymes, thereby resulting in construction of pGP helper-int1. The pGPhelper-int1 construct has a 72 nucleotide region between the GP stopcodon and the 3′ end of the helper (including the 19 nt conservedsequence). To generate a GP helper with only the 19 nucleotide 3′ end,the pCR2.1/GP 19 nt 5′ DNA was digested with SpeI and SphI and the GPcoding sequence ligated into the pGP helper-int1 digested with SpeI andSphI restriction enzymes. The resultant construct was named pGP helper19 nt.

The pGP helper 19 nt construct was then used to produce Δ26S helperswith variable length 3′ replication recognition sequences. The pGPhelper 19 nt construct was digested with NcoI and NotI restrictionenzymes and the 2515 base pair fragment containing the glycoproteincoding sequence with the 19 nt 3′ end region was gel-purified. This 2515base pair (NcoI/NotI) fragment was then ligated into dHgp constructsdigested with NcoI and NotI restriction enzymes, generating the variousdHgp 19 nt constructs.

C. Construction of a Modified Promoterless Helper Cassette Expressingthe Alphavirus Capsid Protein.

In a VEE virus-infected cell, the VEE capsid protein cleaves itself fromthe structural polyprotein that is translated from the 26S subgenomicmRNA. Although the VEE capsid helpers of this invention lack thecomplete glycoprotein coding region, a small portion of the E3 proteinremains on the capsid helper to allow the chymotrypsin-like cleavage tooccur within the packaging cell to produce mature capsid protein.Introduction of a stop codon at the 3′ end of the capsid, in place ofthe chymotrypsin-like cleavage site, would increase the difficulty ofproducing functional recombinants with a glycoprotein helper. That is,for a functional recombination (i.e., one that generates a replicationcompetent virus) to occur with a dHgp helper of this invention, therecombination event would have to be nucleotide perfect to replace theengineered stop codon in the capsid coding sequence and maintain anactive capsid cleavage site. Two versions of dHcap helpers with stopcodons incorporated at the 3′ end were produced. One version,dHcap6-mut1-dSL2 (stop), which has a 3′ sequence provided herein as SEQID NO:57, replaced the C-terminal tryptophan residue of the nativecapsid protein with a stop codon; the other version retained theC-terminal tryptophan residue (dHcap6-mut1 (W-stop), which has a 3′sequence provided herein as SEQ ID NO: 59) and inserted a stop codonimmediately downstream of the tryptophan residue. The capsid codingsequence was amplified with primers designed to engineer a unique RsrIIsite at the 5′ end (Capsid (RsrII-Kozak) F, SEQ ID NO: 91, Table 8) anda unique SphI site at the 3′ end (Capsid (stop) SphI R, SEQ ID NO:92 orCapsid (W-stop) SphI R, SEQ ID NO: 93, Table 8). The forward primer wasalso engineered to place the capsid start codon in a near-optimal Kozakconsensus sequence (Kozak, Cell, 44(2):283-292 (1986)) to enhanceribosome initiation of translation of the capsid mRNA. The amplifiedcapsid coding sequences were digested with RsrII and SphI restrictionenzymes and ligated into Δ26S helper plasmids linearized with RsrII andSphI to produce dHcap6-mut1-dSL2 (stop) and dHcap6-mut1 (W-stop)constructs.

D. Construction of Modified Promoter Helper Cassette ExpressingAlphavirus Glycoproteins.

The VEE capsid protein is a chymotrypsin-like protease that cleavesafter the capsid C-terminal tryptophan residue. On the basis of thecleavage specificity of chymotrypsin, it is expected that all amino acidresidues are tolerated in the position immediately downstream of thetryptophan except methionine and proline. Having either of these aminoacids immediately downstream of the tryptophan is expected to greatlyreduce chymotrypsin cleavage activity. In the native VEE virus, thereare 18 amino acids that comprise the VEE E3 signal sequence. Constructswere designed to reduce the number of amino acids in the E3 signalsequence while maintaining the signaling function of the E3 sequence.Since 16 of the 18 amino acids comprising the E3 sequence are expectedto be tolerated in the position downstream of the capsid C-terminaltryptophan, reducing the number of amino acids in the E3 signal sequencewill reduce the number of sites that would be functional as cleavagesites if they were placed immediately downstream of the C-terminaltryptophan upon the occurrence of a nucleotide-perfect recombinationevent that reconstituted the VEE structural polyprotein coding sequence.As an example of such an approach, the N-terminal serine residuenormally present in the E3 signal sequence was removed by PCR, leaving aleucine residue as the N-terminal residue, and a dHgp promoterlesshelper was constructed to determine if such a modified gp helper wouldfunction to package VRP.

A forward PCR primer (Gp (RsrII-Ser) F, SEQ ID NO: 94) was designed toremove the N-terminal serine residue of E3 and maintain a unique RsrIIrestriction site (Table 8). A reverse PCR primer (3-16.2.14, SEQ ID NO:95) was designed to amplify a gp fragment that would contain a uniqueSnaBI restriction site (Table 8). The resulting gp PCR fragment wasdigested with RsrII and SnaBI and ligated into RsrII and SnaBI digesteddHgp6-mut1 DNA, generating dHgp6-mut1 (-S).

E. VRP Generation Experiments Using 5′ and 3′ Modified Δ26S Helpers

Helpers that contain combinations of the modifications described abovewere also prepared. Different combinations and RNA concentrations of thedHcap and dHgp promoterless helpers were analyzed in VRP productionexperiments to determine how effectively they would package a VEEreplicon RNA (either one expressing the botulinum neurotoxin fragment Aor an influenza HA). In addition, the effect of capping the Δ26S helperson VRP yields was analyzed for a subset of the helper combinations.Representative examples of VRP yields are shown in Tables 9-13 withdifferent combinations of Δ26S helpers. The potency assay to quantitateVRP infectivity and yield is performed in Vero cell monolayer culturesin 48-well plates by serially diluting VRP and incubating with Verocells overnight at 37° C. in 5% CO₂ After overnight incubation (18-20hours), the cells are washed, fixed, and the fixed monolayers stainedwith an antigen-specific primary antibody followed by a FITC-conjugatedsecondary antibody. Cells containing FITC-labeled antigen-antibodycomplexes are detected by ultraviolet fluorescence microscopy (NikonEclipse TE300). Individual antigen-positive cells are counted and thetiter, expressed as IU/mL, is calculated from the known dilution andinoculation volume.

Example 8 Promoterless Helpers Incorporating a Ubiquitin Monomer

A. Construction of Δ26S Helpers Containing Ubiquitin Monomers

In eukaryotic cells, proteins fused or tagged with ubiquitin are cleavedimmediately after its C-terminal glycine by cellular ubiquitincarboxyl-terminal hydrolase (UCH) (Pickart and Rose, J. Biol. Chem260:7903-7910 (1985)). Placing a monomer of the ubiquitin codingsequence in-frame just upstream from the capsid and glycoprotein codingsequences will eliminate the fusion proteins produced with certainpromoterless helper constructs of this invention (such fusions resultingfrom multiple transcriptional start sites upstream of the ATG for eachstructural protein coding sequence). The elimination occurs because allin-frame fusion proteins will include the ubiquitin monomer, and so theywill be cleaved by UCH, thereby releasing full-length VEE structuralproteins without any upstream, exogenous protein sequence. Primersubiquitin F (SEQ ID NO: 96) and ubiquitin R (SEQ ID NO: 97) (Table 14)were designed to introduce RsrII sites at the 5′ and 3′ ends of theamplified ubiquitin monomer coding sequence, while maintaining theArg-Gly-Gly sequence necessary for cleavage of the ubiquitin monomer byUCH (FIG. 4). These particular constructs resulted in additionalN-terminal amino acid residue(s) on each of the resulting structuralproteins following cleavage that are not present on the nativestructural proteins (i.e., for the capsid helper, an extra proline; forthe glycoprotein helper, extra proline and threonine) (FIG. 4).

The ubiquitin coding sequence was PCR amplified using Pfu Taq polymerase(Stratagene) and cloned into the unique RsrII sites of dHcap(FL) anddHgp(FL). Transformants were screened to determine the orientation ofthe ubiquitin insert. Positive ubiquitin clones for capsid andglycoprotein, designated dHcapU and dHgpU, respectively (and with 5′ endsequences provided herein as SEQ ID NOS. 53 and 54, respectively), wereisolated and sequenced to confirm that no errors were introduced intothe amplified ubiquitin coding sequence. RNAs for electroporation weretranscribed in separate reactions from dHcapU, dHgpU, dHcap(FL),dHgp(FL), Hcap4, and 13.4.6 plasmids using the RiboMax Express RNA® kitand precipitated with lithium chloride.

B. VRP Generation Experiments Using Ubiquitin Modified Δ26S Helpers

Vero cells were electroporated with a VEE replicon RNA expressing an HIVclade C glycoprotein (“DU151gp160”) and selected combinations ofpromoterless capsid and GP helpers at the indicated RNA amounts. In someexperiments, the “Hcap4” capsid helper was used. This is a helper thathas a truncated 5′ end (corresponding to the dHcap4 truncation describedhereinabove) but retains the 26S subgenomic promoter sequence and isfully described in U.S. Pat. No. 7,045,335, which is incorporated hereinby reference. Electroporations were performed at 500V, 25 μF, 4 pulsesin a 0.4 cm cuvette in a volume of approximately 0.8 ml. Eachelectroporation was seeded into 1-850 cm² roller bottle with 100 mlOptipro® (Gibco, Carlsbad, Calif.). VRP were harvested at 18 hrs on a0.2 μm filter with 25 ml of 0.5M NaCl wash. VRP salt wash material wastitered with the anti-gp120 goat antibody (which recognizes the HIV gp160 protein) at 1:400. Results of packaging experiments are shown inTable 15.

Electroporations were subsequently performed to compare titers ofvarious nucleic acids packaged with capsid helpers dHcapU ordHcap6-mut1(W-stop) combined with dHgp6-mut1. VRPs were titered using aVEE nsP2 specific polyclonal antibody (Table 16).

C. Structural Protein Expression by Western analysis in ElectroporatedCells

Cell lysates were prepared from the cells used to generate VRP in thepackaging study summarized in Table 16. Cell lysates from each samplewere electrophoresed in 4-12% Bis-Tris Novex gels at 200V, 400 mA in1×MOPS for 45 min prior to semidry transfer to PVDF at 400 mA in 1×transfer buffer for 40 min. Membranes were blocked overnight in 1×BMBblock/TBS. Primary antibodies were a 1:500 dilution of 1A4A anti-VEE GPand a 1:1500 dilution of anti-VEE capsid in 1×BMB block/TBS. Westernblot results are shown in FIG. 5. The glycoprotein expressed from dHgpUis processed into the PE2 and E2 GP forms more completely than theglycoprotein expressed from dHgp(FL). This is demonstrated by thedifference in the pattern of fusion proteins seen without the ubiquitinpresent in dHgp(FL) (FIG. 5, compare lanes 3 and 4 on the Western blotusing GP antibody). Placement of the ubiquitin protein at the N-terminusof the capsid protein in the dHcapU helper resulted in the disappearanceof the capsid fusion proteins (FIG. 5) and a greater than 2 log increasein gp160 titer when packaged with the 13.4.6 glycoprotein helper (Table15).

D. Structural Protein RNA Expression by Northern Analysis ofElectroporated Cells

Total cellular RNA was extracted from the cells used to generate VRP inthe packaging study summarized in Table 15. The cells were lysed withRNAwiz® reagent (Ambion, Inc., Austin, Tex.), extracted with chloroform,precipitated, and subjected to Northern analysis using capsid and GPspecific probes (FIG. 6 and FIG. 7, respectively). All RNA species areconsistent with the sizes expected from the various constructs.

Example 9 VRP Generation Using Capped and Non-Capped Δ26S HelperConstructs

A. VRPs Expressing the Glycoproteins of Various Alphaviruses

VRPs were produced using VEE replicons that express, as the nucleic acidof interest (NOI), the coding sequence for the glycoproteins of eitherVEE (3022), Eastern equine encephalitis virus (EEE) (4200) or Westernequine encephalitis virus (WEE) (2100), in which each furin cleavagesite has been deleted. DNA plasmids encoding the helpers used togenerate the VRP were linearized with NotI and in vitro transcribedusing a T7 RiboMax® kit (Promega, Madison Wis.) following themanufacturer's instructions, and where indicated, supplemented with 7.5mM CAP analog (Promega). Helpers produced with cap analog are indicatedas “+Cap” and those without cap analog are indicated as “−Cap” in Table17. Vero cells were electroporated with combinations of replicon, capsidhelper and GP helper RNAs and VRP were produced as described in Example5 hereinabove. The results of three separate experiments are shown inTables 17-19.

B. VRP Expressing the HA Coding Sequence of Influenza Strain Wisconsin

In this experiment, the molar ratios of the Cap analog to GTP werevaried in the transcription reactions for producing Δ26S helper RNAsencoding either VEE capsid or VEE glycoproteins. The transcriptionreactions were assembled as follows: Promega 5× transcription buffer;rNTP mix (6 mM UTP, CTP, ATP); GTP (at 0-6 mM, as indicated in thetable); (Promega Corporation Woods Hollow Rd., Madison Wis., catalog#P1300) and Ribo m⁷G Cap® analog (6 mM) (Promega Corporation WoodsHollow Rd., Madison Wis., catalog #P1712). Additional reactions weremade with Promega's 5× buffer and 7.5 mM rNTPs with and without 7.5 mMRibo m⁷G Cap analog to mimic the T7 RiboMAX Express® RNA transcriptionkit conditions (Promega Corporation Woods Hollow Rd., Madison Wis.,catalog #P1320) specified by the manufacturer, which is typically runwith the 2× buffer supplied with the kit. The VEE replicon that waspackaged in this experiment encoded the influenza HA (A/WI/05) protein.Thirty μg of the replicon RNA; 10 μg of a Δ26S capsid helper RNA, and 60μg of a Δ26S glycoprotein helper RNA were used for each electroporation.Vero cells were expanded, then washed and resuspended in sucrose bufferto 1.2×10⁸ cells/mL. These cells were mixed with the RNAs, thenelectroporated with the BioRad Gene Pulse II® apparatus set to 500volts, 25 μFd and four pulses. Cells were transferred to roller bottleswith 100 mL OptiPro® and incubated at 37° C. Twenty-four hourspost-electroporation, VRPs were harvested. The VRPs were titered on48-well plates of Vero and results are shown in Table 25.

Example 10 Protection Against Botulinum Neurotoxins in Mice Using VRPsMade with Δ26S Helper Constructs

VEE replicon vectors that express the non-toxic c-terminal fragment ofthe heavy chain of either botulinum neurotoxin serotype A or B (BoNT Aor BoNT B, respectively) were packaged into VRPs using either: (i) 30 μgeach of uncapped 13.2.2 and 13.4.6 helpers, or (ii) 20 μg of the cappedcapsid Δ26S helper and 60 μg of the capped glycoprotein Δ26S helper, asdescribed in Example 5. These VRPs were used at a dose of 1×10⁷ IU tovaccinate Swiss mice two times at day 0 and day 28. The mice were thenchallenged with 1000 times the dose required to kill 50 percent ofanimals (1000 LD₅₀) of either BoNT A or BoNT B neurotoxin one monthafter the second immunization. The results of the challenge experimentare summarized in Table 20.

Example 11 Immunogenicity and Protection Studies with VRPs ExpressingAntigens from the Smallpox Virus

A. Immunogenicity in Mice and Primates of VRP Generated Using Δ26SHelper Constructs.

VEE replicon vectors optimized to express four vaccinia virus (VACV)genes (L1R, B5R, A27L and A33R) were constructed using the methoddescribed by Kamrud et al. (Virology 360(2):376-87 (2007)). The fourVACV genes are collectively referred to as “4pox.” The 4pox genes werecloned into two different VEE replicon vector systems, one based on the3014 strain of VEE and the other based on the TC-83 vaccine strain. Eachoptimized VACV coding sequence-expressing replicon vector was used togenerate VRPs by combining 30 μg of the replicon, 20 μg of Δ26S capsidhelper RNA, and 60 μg of Δ26S GP helper RNA and electroporating theminto Vero cells. Particles were produced and collected as described inExample 5. The individual VACV VRPs were then combined, producing a 4poxVRP mixture used to immunize either BALB/c mice or Cynomolgus macaquesand the humoral responses were measured by VACV antigen-specific ELISAanalysis. The VACV-specific ELISA responses detected in vaccinated miceare shown in Table 21 and the VACV-specific ELISA responses detected invaccinated macaques are shown in Table 22.

B. Protection in Mice and Non-Human Primates Using the 4pox VRPs

1. Mice

Mice were challenged by the intranasal route with 2×10⁶ PFU of vacciniavirus (strain IHD-J), and the results are presented in Table 23.

2. Non-Human Primates

Non-human primates were challenged by the intravenous route with 5×10⁶PFU of monkeypox virus. The World Health Organization's lesion countscoring system was used to determine disease severity, and the resultsare presented in Table 24.

As will be understood by one skilled in the art, there are severalembodiments and elements for each aspect of the claimed invention, andall combinations of different elements are incorporated herein asembodiments of this invention, so the specific combinations exemplifiedherein are not to be construed as limitations in the scope of theinvention as claimed. If specific elements are removed or added to thegroup of elements available in a combination, then the group of elementsis to be construed as having incorporated such a change.

All references cited herein, including non-patent publications, patentapplications, and patents, are incorporated by reference herein in theirentireties to the same extent as if each was individually andspecifically indicated to be incorporated by reference, and wasreproduced in its entirety herein.

TABLE 1 Primers to generate Δ26S helpers SEQ Primer ID name 5′ primersequence 3′ NO: Capsid F CCTCGGACCGATGTTCCCGTTCCAGCCAATG 98 GP FCCTCGGACCGACCATGTCACTAGTGACCACCATG 60 13-101.pr4TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 61TTTTTTTTTGAAATATTAAAAACAAAATCCGATTCG G 3-16.1.1 ACCGTCACCCTGGATGCTGT 62dHe1p1 R CCTCGGACCGAAACAGCGACTTGCCCTTCGTAGCGA 63 CAC dHe1p2 RCCTCGGACCGCATAGTCTCAGTTTCCAGGTCAGGGT 64 CGC dHe1p3 RCCTCGGACCGCGGCGAGCTCCTTCATTTTCTTGTCC 65 AATTCCT dHe1p4 RCCTCGGACCGCAGCTTAGTTGCATACTTATACAATC 66 TGTCCGGA dHe1p5 RCCTCGGACCGACATCTCATCGGACAGATACAATGAT 67 ACTTGTGCT dHe1p6 RCCTCGGACCGTCCAATGTCAAGGATCGTGTCGGATG 68 GGT dHe1p7 RCCTCGGACCGAGTTTTGAAGCCAGATGCGAAAACGC 69 TCTG dHe1p8 RCCTCGGACCGCTTGGCTTCTACCTCAAACTGCGGGA 70 AGC

TABLE 2 IFA analysis of dHcap1-8 helpers Helper Anti-capsid IFA dHcap1Positive dHcap2 Positive dHcap3 Positive dHcap4 Positive dHcap5 PositivedHcap6 Positive dHcap7 Positive dHcap8 Positive (weak)

TABLE 3 Helper Anti-GP IFA DHgp1 Positive dHgp2 Positive dHgp3 PositivedHgp4 Positive dHgp5 Positive dHgp6 Positive dHgp7 Positive dHgp8Negative

TABLE 4 Site directed mutagenesis primers to generate mut1 helpers SEQPrimer ID name 5′ primer sequence 3′ NO Mut1 FGACCAATTACCTACCCAAATAGGAGAAAGTTCACGT 71 TGAC Mut1 RGTCAACGTGAACTTTCTCCTATTTGGGTAGGTAATT 72 GGTC

TABLE 5 Primers used to change 5′ replication recogni- tion sequence ATGcodons to GTG Primer name (location of SEQ A residue ID in ATG codon)5′ primer sequence 3′ NO nt- 12 ATAGGCGGCGCGTGAGAGAAGCCCAG 73 nt-45CCTACCCAAAGTGGAGAAAGTTCACGTTG 74 ACATC nt-148/154/160CAGGTCACTGATAGTGACCGTGCTAGTGC 75 CAGAGCG nt-259GCCCGCCCGCAGAGTGTATTCTAAGCAC 76 nt-295/300 GTATCTGTCCGGTGAGGTGTGCGGAAGAT77 CCG nt-331 GACAGATTGTATAAGTGTGCAACTAAGCT 78 G nt-390GAATGGACAAGAAAGTGAAGGAGCTC 79 nt-411 CCGTCGTGAGCGACCCTGACCTGGAAAC 80nt-441 GAAACTGAGACTGTGTGCCTCCACG 81 nt-499 GTTTACCAGGGTGTATACGCGGTTG 82

TABLE 6 Capsid helper GP helper VRP yield BoNT B replicon dHcap6 mut1(30 μg) 13.4.6 (30 μg) 9.0 × 10⁹ BoNT A replicon dHcap6 (30 μg) dHgp7(30 μg) 6.0 × 10⁹ dHcap6 (30 μg) dHgp7 (90 μg) 2.6 × 10¹⁰ BoNT Areplicon dHcap5-mm (30 μg) dHgp6 mut1 (90 μg) 1.8 × 10⁷ dHcap6-mm (30μg) dHgp6 mut1 (90 μg) 3.6 × 10⁸ dHcap7-mm (30 μg) dHgp6 mut1 (90 μg)1.3 × 10⁸ dHcap4 mut1 (30 μg) dHgp6 mut1 (90 μg) 1.3 × 10⁹ dHcap6 mut1(30 μg) dHgp6 mut1 (90 μg) 4.6 × 10⁹ dHcap7 mut1 (30 μg) dHgp6 mut1 (90μg) 6.2 × 10⁹ dHcap5-mm (10 μg) dHgp6 mut1 (90 μg) 4.2 × 10⁶ dHcap6-mm(10 μg) dHgp6 mut1 (90 μg) 2.6 × 10⁸ dHcap7-mm (10 μg) dHgp6 mut1 (90μg) 4.4 × 10⁷ dHcap4 mut1 (10 μg) dHgp6 mut1 (90 μg) 1.1 × 10¹⁰ dHcap6mut1 (10 μg) dHgp6 mut1 (90 μg) 1.9 × 10¹⁰ dHcap7 mut1 (10 μg) dHgp6mut1 (90 μg) 1.8 × 10¹⁰ SARS S replicon dHcap4 mut1 (10 μg) dHgp6 mut1(90 μg) 4.4 × 10⁹ dHcap6 mut1 (10 μg) dHgp6 mut1 (90 μg) 2.6 × 10⁹dHcap7 mut1 (10 μg) dHgp6 mut1 (90 μg) 1.4 × 10⁹ BoNT A replicon dHcap1(30 μg) 13.4.6 (30 μg) 3.0 × 10⁷ dHcap2 (30 μg) 13.4.6 (30 μg) 9.2 × 10⁷dHcap3 (30 μg) 13.4.6 (30 μg) 2.0 × 10⁸ dHcap4 (30 μg) 13.4.6 (30 μg)1.3 × 10⁹ dHcap5 (30 μg) 13.4.6 (30 μg) 3.2 × 10⁸ dHcap6 (30 μg) 13.4.6(30 μg) 3.0 × 10⁸ dHcap7 (30 μg) 13.4.6 (30 μg) 1.2 × 10⁹ dHcap8 (30 μg)13.4.6 (30 μg) 1.8 × 10⁷ dHcap6 mut1 (30 μg) 13.4.6 (30 μg) 8.4 × 10⁹dHcap6 mut1 (30 μg) 13.4.6 (30 μg) 1.2 × 10¹⁰

TABLE 7 VRP yield generated using Δ26S capsid, E1 and E2 helpers.pERK/342/MS/BoNT A [30 μg] VRP Capsid helper GP helper #1 GP helper #2titer/ml dHcap6-mut1 [10 μg] dHE1-6M1 [30 μg] dHE2-6M1 2.2 × 10⁷ [30 μg]dHcap6-mut1 [10 μg] dHgp7-mut1 [90 μg] 1.3 × 10⁹

TABLE 8 PCR primers used to design modifications to the 5′ and3′ regions of Δ26S helpers SEQ ID Primer name 5′ primer sequence 3′ NO:13-82.1.9 TCAGTGGAACGAAAACTCACG 83 dSL2 (EcoRV) RTTTGATATCGGTAATTGGTCTGGGCTTCTC 84 dSL2 (EcoRV) FTTTGATATCGAAGCCAAGCAGGTCACTG 85 3-8.pr4 GCAACGCGGGGAGGCAGACA 86 GP(SphI) R GCATGCTCAATTATGTTTCTGGTTGG 87 3-16.1.3 CGACATAGTCTAGTCCGCCA 883′ trunc GCATGCATTTTGTTTTTAATATTTCAAA 89 (SphI) F 3′ truncGCTCACATGTTCTTTCCTGCG 90 (AfIIII) R Capsid (RsrII-CCTCGGACCGACCATGTTCCCGTTCCAGCC 91 Kozak) F AATG Capsid (stop)ACATGCATGCTTATTGCTCGCAGTTCTCCGG 92 SphI R Capsid (W-stop)ACATGCATGCTTACCATTGCTCGCAGTTCTC 93 SphI R CGG Gp (RsrII-Ser)CCTCGGTCCGACCATGCTAGTGACCACCAT 94 F G 3-16.2.14 ACATACACGGTAGTCACAAT 95

TABLE 9 Replicon packaged pERK/342/MS/BoNT A [30 μg RNA] Capsid helper[RNA] GP helper [RNA] VRP titer IFU/ml dHcap7-mut1 (W-stop) [10 μg]dHgp7-mut1 [90 μg] 1.0 × 10⁸ dHcap6-mut1 (W-stop) [10 μg] dHgp7-mut1 [90μg] 8.9 × 10⁸ dHcap7-mut1 (W-stop) [20 μg] dHgp7-mut1 [90 μg] 3.0 × 10⁸dHcap6-mut1 (W-stop) [20 μg] dHgp7-mut1 [90 μg] 6.8 × 10⁸

TABLE 10 Replicon packaged pERK/342/MS/BoNT A [30 μg RNA] VRP titerCapsid helper [RNA] GP helper [RNA] IFU/ml dHcap6-mut1 [10 μg]dHgp7-mut1 [60 μg] 2.1 × 10⁸ dHcap6-mut1 (W-stop) [10 μg] dHgp7-mut1 [60μg] 2.0 × 10⁸ dHcap6-mut1 (W-stop)-dSL2 [10 μg] dHgp7-mut1 [60 μg] 3.7 ×10⁷

TABLE 11 Replicon packaged pERK/342/MS/BoNT A [30 μg RNA] Capsid helper[RNA] GP helper [RNA] VRP titer IFU/ml dHcap7-mut1 [20 μg] dHgp7-mut1[90 μg] 4.9 × 10⁷ dHcap7-mut1 19nt [30 μg] dHgp7-mut1 [90 μg] 2.2 × 10⁷

TABLE 12 Replicon packaged pERK/342/MS/BoNT A [30 μg RNA] Capsid helper[RNA] Glycoprotein helper [RNA] VRP titer [10 μg] [60 μg] IFU/mldHcap7-mut1 (W-stop) dHgp6-mut1 6.1 × 10⁶ dHcap7-mut1 (W-stop)dHgp6-mut1-dSL2 (-S) 6.6 × 10⁵ dHcap7-mut1 (W-stop) dHgp6-mut1-dSL2 (-S)19 nt 9.6 × 10⁴ dHcap7-mut1 (W-stop) dHgp6-mut1 (-S) 1.0 × 10⁷dHcap6-mut1 (W-stop) dHgp6-mut1 2.7 × 10⁷ dHcap6-mut1 (W-stop)dHgp6-mut1-dSL2 (-S) 1.7 × 10⁶ dHcap6-mut1 (W-stop) dHgp6-mut1-dSL2 (-S)19 nt 1.2 × 10⁵ dHcap6-mut1 (W-stop) dHgp6-mut1 (-S) 2.2 × 10⁷

TABLE 13 pERK/383/MS/HA (A Wyoming) [30 μg RNA] VRP titer Capsid helper[RNA] GP helper [RNA] IFU/ml dHcap6-mut1 (W-stop) [20 μg] dHgp6-mut1 [60μg] 2.0 × 10⁸ dHcap6-mut1 (W-stop) capped dHgp6-mut1 capped 9.0 × 10⁹[20 μg] [60 μg] dHcap6-mut1 (W-stop) [10 μg] dHgp6-mut1 [90 μg] 2.5 ×10⁷ dHcap6-mut1 (W-stop) capped dHgp6-mut1 capped 2.5 × 10⁸ [10 μg] [90μg] dHcap6-mut1 (W-stop) [10 μg] dHgp6-mm [90 μg] 2.3 × 10⁷ dHcap6-mut1(W-stop) capped dHgp6-mm capped 2.4 × 10⁸ [10 μg] [90 μg]

TABLE 14 SEQ Primer ID name 5′ primer sequence 3′ NO: Ubiquitin FCATCGACGGACCGATGCAGATCTTCGTGAAGA 96 CCC Ubiquitin RGATTTTCGGTCCGCCCCTCAGACGGAGGACCA 97 GG

TABLE 15 VRP generation using ubiquitin-modified Δ26S helpercombinations Replicon RNA Glycoprotein VRP [30 μg] Capsid helper helper[60 μg] titer/ml DU151gp160 dHcap(FL) [10 μg] 13.4.6 8.3 × 10⁵DU151gp160 dHcapU [10 μg] 13.4.6 1.3 × 10⁸ DU151gp160 Hcap4 [30 μg]dHgp6-mut1 9.3 × 10⁷ DU151gp160 dHcap6-mut1 (W-stop) 13.4.6 5.6 × 10⁸[10 μg]

TABLE 16 VRP generation using multiple replicon vectors and modifiedΔ26S helper combinations Replicon RNA VRP [30 μg] Capsid helper [10 μg]GP helper [60 μg] titer/ml BoNT A dHcapU dHgp6-mut1 1.4 × 10⁸ BoNT AdHcap6-mut1 (W-stop) dHgp6-mut1 3.6 × 10⁸ BoNT E dHcapU dHgp6-mut1 3.2 ×10⁷ BoNT E dHcap6-mut1 (W-stop) dHgp6-mut1 1.4 × 10⁸ HA (A Wyoming)dHcapU dHgp6-mut1 3.8 × 10⁸ HA (A Wyoming) dHcap6-mut1 (W-stop)dHgp6-mut1 6.4 × 10⁸ NA (A Wyoming) dHcapU dHgp6-mut1 4.0 × 10⁸ NA (AWyoming) dHcap6-mut1 (W-stop) dHgp6-mut1 5.3 × 10⁸ CEA dHcapU dHgp6-mut12.0 × 10⁸ CEA dHcap6-mut1 (W-stop) dHgp6-mut1 3.1 × 10⁸

TABLE 17 Comparison of use of Capped vs. Non-capped Helpers NOI in VEEreplicon Helpers +/−Cap IU/cell VEE glycoprotein 3022 13.2.2; 13.4.6−Cap 131.1 VEE glycoprotein 3022 13.2.2; 13.4.6 +Cap 1095.4 VEEglycoprotein 3022 Δ26S helpers (C & GP) −Cap 49.0 VEE glycoprotein 3022Δ26S helpers (C & GP) +Cap 508.8 EEE glycoprotein 4200 13.2.2; 13.4.6−Cap 30.7 EEE glycoprotein 4200 13.2.2; 13.4.6 +Cap 398.8 EEEglycoprotein 4200 Δ26S helpers (C & GP) −Cap 9.3 EEE glycoprotein 4200Δ26S helpers (C & GP) +Cap 88.0

TABLE 18 NOI in VEE replicon Helpers +/−Cap IU/cell VEE glycoprotein3022 13.2.2; 13.4.6 −Cap 600.4 VEE glycoprotein 3022 13.2.2; 13.4.6 +Cap2035.0 VEE glycoprotein 3022 Δ26S helpers (C & GP) −Cap 101.3 VEEglycoprotein 3022 Δ26S helpers (C & GP) +Cap 884.6 EEE glycoprotein 420013.2.2; 13.4.6 −Cap 75.2 EEE glycoprotein 4200 13.2.2; 13.4.6 +Cap 898.3EEE glycoprotein 4200 Δ26S helpers (C & GP) −Cap 29.8 EEE glycoprotein4200 Δ26S helpers (C & GP) +Cap 206.3

TABLE 19 Δ26S Capsid Δ26S GP NOI in VEE replicon Helper (+/−cap) Helper(+/−cap) IU/cell WEE glycoprotein 2100 −cap −cap 37.1 WEE glycoprotein2100 +cap +cap 285.7 WEE glycoprotein 2100 +cap −cap 38.6 WEEglycoprotein 2100 −cap +cap 34.3

TABLE 20 Results from challenge of mice vaccinated with VRP producedusing Δ26S helpers Survival Survival Replicon (helper set) BoNT-A/totalBoNT-B/total MS/342/BoNT A (13.2.2 + 13.4.6) 8/10 NA MS/342/BoNT A (Δ26Scapsid + gp) 10/10  NA Control VRP¹ 0/10 NA MS/357/BoNT B (13.2.2 +13.4.6) NA 10/10  MS/357/BoNT B ((Δ26S capsid + gp) NA 8/10 Control VRP¹NA 0/10 NA: not applicable ¹Contains irrelevant protein-expressingcoding sequence in replicon

TABLE 21 Replicon Log10 VACV-specific ELISA titer expressing 4pox Dose(IU) L1R B5R A27L A33R V3014 1 × 10⁶ 2 3 1 3 TC-83 1 × 10⁶ 3 4 1 4 V30141 × 10⁷ 3 4 3 4 TC-83 1 × 10⁷ 4 4 1 4

TABLE 22 Replicon Log10 VACV-specific ELISA titer expressing 4pox Dose(IU) L1R B5R A27L A33R TC-83 1 × 10⁸ 3.2 2.4 2.2 3.2 V3014 1 × 10⁸ 3.62.6 2 3.6

TABLE 23 Protection Study in Mice VRP vaccine # mice tested % survivalV3014 4pox 48 100% V3014 control 24 0% TC-83 4pox 40 100% TC-83 control24 9%

TABLE 24 Protection study in Macaques VRP Challenge Max pock VaccineSystem Animal # Outcome * count 4pox VRP V3014 1 No disease 0 2 Milddisease 2 3 Mild disease 8 4 Mild disease 4 5 Mild disease 12 4pox VRPTC-83 1 No disease 0 2 Mild disease 8 3 Mild disease 12 4 Mild disease10 5 Mild disease 8 Control V3014 1 Lethal disease TNTC¹ VRP 2 Lethaldisease TNTC 3 Lethal disease TNTC Control TC-83 1 Lethal disease TNTCVRP 2 Grave disease TNTC 3 Severe disease >100 ¹TNTC = too numerous tocount

TABLE 25 Study of effects of capping of Δ26S helpers on packaging of analphavirus replicon vector encoding the HA coding sequence frominfluenza strain Wisconsin. Buffer used in in vitro transcriptionCap:GTP ratio Titer IU/ EP reactions Capsid GP IU/mL Total IU cell 1 5X0:1 0:1 3.70E+08 9.26E+09 154 2 5X 1:1 0:1 4.66E+08 1.16E+10 194 3 5X2:1 0:1 3.52E+08 8.80E+09 147 4 5X 4:1 0:1 3.70E+08 9.26E+09 154 5 5X6:1 0:1 3.81E+08 9.54E+09 159 6 5X 0:1 1:1 1.91E+08 4.77E+09 79 7 5X 1:11:1 4.44E+08 1.11E+10 185 8 5X 2:1 1:1 4.88E+08 1.22E+10 203 9 5X 4:11:1 4.36E+08 1.09E+10 182 10 5X 6:1 1:1 4.36E+08 1.09E+10 182 11 5X 0:12:1 1.17E+08 2.93E+09 49 12 5X 1:1 2:1 3.04E+08 7.61E+09 127 13 5X 2:12:1 3.04E+08 7.61E+09 127 14 5X 4:1 2:1 3.37E+08 8.44E+09 141 15 5X 6:12:1 4.14E+08 1.04E+10 173 16 5X 0:1 4:1 1.71E+08 4.26E+09 71 17 5X 1:14:1 7.56E+08 1.89E+10 315 18 5X 4:1 4:1 4.66E+08 1.16E+10 194 19 5X 0:16:1 1.72E+08 4.31E+09 72 20 5X 6:1 6:1 4.03E+08 1.01E+10 168 21 5X 1:10:1 4.36E+08 1.09E+10 182 22 5X 0:1 1:1 1.60E+08 3.99E+09 66 23 5X 2:12:1 5.10E+08 1.27E+10 212 24 2X 0:1 1:1 1.80E+08 4.49E+09 75 (7.5 mM)(7.5 mM) 25 2X 1:1 0:1 3.56E+08 8.89E+09 148 (7.5 mM) (7.5 mM) 26 5X 1:11:1 6.82E+08 1.71E+10 284 (7.5 mM) (7.5 mM) 27 2X 1:1 1:1 7.04E+081.76E+10 293 (7.5 mM) (7.5 mM) 28 2X 1:1 1:1 6.24E+08 1.56E+10 260 (7.5mM) (7.5 mM) 29 2X 0:1 0:1 3.30E+08 8.25E+09 138 (7.5 mM) (7.5 mM) 30 2X0:1 0:1 3.41E+08 8.53E+09 142 (7.5 mM) (7.5 mM)

1. An isolated RNA molecule comprising: a) an alphavirus 5′ replicationrecognition sequence, wherein at least one initiation codon has beenremoved from the 5′ replication recognition sequence; b) a nucleotidesequence encoding an alphavirus structural protein; and c) an alphavirus3′ replication recognition sequence, with the proviso that the RNAmolecule does not contain a promoter that directs transcription of thenucleotide sequence of (b), and wherein the alphavirus 5′ and 3′replication recognition sequences of (a) and (c) direct replication ofthe entire RNA molecule in the presence of alphavirus nonstructuralproteins.
 2. The RNA molecule of claim 1, wherein the nucleotidesequence encoding the alphavirus structural protein is selected from thegroup consisting of a nucleotide sequence encoding 1) an alphaviruscapsid protein, 2) alphavirus E1 and E2 proteins in any order, 3)alphavirus capsid protein and alphavirus E1 protein in any order, 5)alphavirus capsid protein and alphavirus E2 protein in any order, 6)alphavirus E2 protein, and 7) alphavirus E1 protein.
 3. The RNA moleculeof claim 1, wherein the alphavirus 5′ replication recognition sequenceis the 5′ replication recognition sequence of Venezuelan equineencephalitis virus.
 4. The RNA molecule of claim 3, wherein the 5′replication recognition sequence is between 70 and 524 nucleotides inlength.
 5. The RNA molecule of claim 1, wherein the alphavirus 3′replication recognition sequence is the 3′ replication recognitionsequence of Venezuelan equine encephalitis virus.
 6. The RNA molecule ofclaim 3, wherein the alphavirus 3′ replication recognition sequence isthe 3′ replication recognition sequence of Venezuelan equineencephalitis virus.
 7. The RNA molecule of claim 1, wherein the 3′replication recognition sequence is 19 to 325 nucleotides in length. 8.The RNA molecule of claim 1, wherein the at least one initiation codonis the initiation codon for nonstructural protein 1 (nsp1).
 9. The RNAmolecule of claim 1, wherein all initiation codons have been removedfrom the 5′ replication recognition sequence.
 10. The RNA molecule ofclaim 1, wherein the RNA is capped at the 5′ terminus.
 11. A populationof alphavirus replicon particles, comprising a subset of particlescomprising the RNA molecule of claim 1, wherein the population containsno detectable replication-competent alphavirus virus particles per 10⁸alphavirus replicon particles, as determined by passage on permissivecells in culture.
 12. A population of alphavirus replicon particles,comprising a subset of particles comprising the RNA molecule of claim 1,wherein the population contains no detectable replication-competentalphavirus particles per 10⁸ alphavirus replicon particles, asdetermined by passage on permissive cells in culture, wherein thealphavirus replicon particles comprise one or more attenuating mutationsin either an alphavirus structural protein or an alphavirusnonstructural protein or both an alphavirus structural protein and analphavirus nonstructural protein.
 13. A composition comprising thepopulation of claim 11 in a pharmaceutically acceptable carrier.
 14. Acomposition comprising the population of claim 12 in a pharmaceuticallyacceptable carrier.
 15. A method of inducing an immune response in asubject, comprising administering an effective amount of the populationof claim 11 to the subject.
 16. A method of inducing an immune responsein a subject, comprising administering an effective amount of thepopulation of claim 12 to the subject.
 17. An isolated cell comprisingthe RNA molecule of claim
 1. 18. A vector comprising the RNA molecule ofclaim
 1. 19. A nucleic acid construct comprising the RNA molecule ofclaim
 1. 20. An isolated cell comprising the vector of claim
 18. 21. Anisolated cell comprising the nucleic acid construct of claim 19.